diff --git a/.ipynb_checkpoints/bash_class_assignment-checkpoint.ipynb b/.ipynb_checkpoints/bash_class_assignment-checkpoint.ipynb new file mode 100644 index 0000000..62dcca0 --- /dev/null +++ b/.ipynb_checkpoints/bash_class_assignment-checkpoint.ipynb @@ -0,0 +1,563 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# `bash` practicals\n", + "\n", + "## Directory and file structure\n", + "\n", + "Using one command move to your home directory." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "cd" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Change your directory on your local drive (mounted from virtualbox). " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Confirm that you are in the correct location." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/home/trinleb\n" + ] + } + ], + "source": [ + "pwd" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Download the data required for the class. The files are `split` into two part because of GitHub limitation." + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "--2021-09-01 20:42:23-- https://github.com/cb2edu/CB2-101-BioComp/raw/2020/01-Linux_101/data/linux_data.tar.xz.partaa\n", + "Resolving github.com (github.com)... 140.82.113.4\n", + "Connecting to github.com (github.com)|140.82.113.4|:443... connected.\n", + "HTTP request sent, awaiting response... 302 Found\n", + "Location: https://raw.githubusercontent.com/cb2edu/CB2-101-BioComp/2020/01-Linux_101/data/linux_data.tar.xz.partaa [following]\n", + "--2021-09-01 20:42:23-- https://raw.githubusercontent.com/cb2edu/CB2-101-BioComp/2020/01-Linux_101/data/linux_data.tar.xz.partaa\n", + "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.110.133, 185.199.111.133, ...\n", + "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.\n", + "HTTP request sent, awaiting response... 200 OK\n", + "Length: 94371840 (90M) [application/octet-stream]\n", + "Saving to: ‘linux_data.tar.xz.partaa’\n", + "\n", + "100%[======================================>] 94,371,840 80.4MB/s in 1.1s \n", + "\n", + "2021-09-01 20:42:25 (80.4 MB/s) - ‘linux_data.tar.xz.partaa’ saved [94371840/94371840]\n", + "\n", + "--2021-09-01 20:42:25-- https://github.com/cb2edu/CB2-101-BioComp/raw/2020/01-Linux_101/data/linux_data.tar.xz.partab\n", + "Resolving github.com (github.com)... 140.82.113.4\n", + "Connecting to github.com (github.com)|140.82.113.4|:443... connected.\n", + "HTTP request sent, awaiting response... 302 Found\n", + "Location: https://raw.githubusercontent.com/cb2edu/CB2-101-BioComp/2020/01-Linux_101/data/linux_data.tar.xz.partab [following]\n", + "--2021-09-01 20:42:25-- https://raw.githubusercontent.com/cb2edu/CB2-101-BioComp/2020/01-Linux_101/data/linux_data.tar.xz.partab\n", + "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.110.133, 185.199.111.133, ...\n", + "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.\n", + "HTTP request sent, awaiting response... 200 OK\n", + "Length: 40809432 (39M) [application/octet-stream]\n", + "Saving to: ‘linux_data.tar.xz.partab’\n", + "\n", + "100%[======================================>] 40,809,432 74.6MB/s in 0.5s \n", + "\n", + "2021-09-01 20:42:26 (74.6 MB/s) - ‘linux_data.tar.xz.partab’ saved [40809432/40809432]\n", + "\n" + ] + } + ], + "source": [ + "wget https://github.com/cb2edu/CB2-101-BioComp/raw/2020/01-Linux_101/data/linux_data.tar.xz.partaa\n", + "wget https://github.com/cb2edu/CB2-101-BioComp/raw/2020/01-Linux_101/data/linux_data.tar.xz.partab" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Check that there are two files in the directory." + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "bash_class_assignment.ipynb linux_data\n", + "git_practicals.ipynb\t linux_data.tar.xz\n", + "igv\t\t\t linux_data.tar.xz.partaa\n", + "info302\t\t\t linux_data.tar.xz.partab\n", + "info302_assignment\t problematic_sites_sarsCov2.vcf\n" + ] + } + ], + "source": [ + "ls" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Join the parts." + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "bash_class_assignment.ipynb linux_data\n", + "git_practicals.ipynb\t linux_data.tar.xz\n", + "igv\t\t\t linux_data.tar.xz.partaa\n", + "info302\t\t\t linux_data.tar.xz.partab\n", + "info302_assignment\t problematic_sites_sarsCov2.vcf\n" + ] + } + ], + "source": [ + "cat linux_data.tar.xz.parta* > linux_data.tar.xz\n", + "ls" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We don't need the parts anymore." + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "rm linux_data.tar.xz.parta*" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Unzip the data." + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "._linux_data\n", + "linux_data/\n", + "linux_data/._raw_fastq\n", + "linux_data/raw_fastq/\n", + "linux_data/._.DS_Store\n", + "linux_data/.DS_Store\n", + "linux_data/._other\n", + "linux_data/other/\n", + "linux_data/._genomics_data\n", + "linux_data/genomics_data/\n", + "linux_data/._reference_data\n", + "linux_data/reference_data/\n", + "linux_data/._.my_hidden_directory\n", + "linux_data/.my_hidden_directory/\n", + "linux_data/.my_hidden_directory/._hidden.txt\n", + "linux_data/.my_hidden_directory/hidden.txt\n", + "linux_data/reference_data/._chr1.fa\n", + "linux_data/reference_data/chr1.fa\n", + "linux_data/reference_data/._chr1-hg19_genes.gtf\n", + "linux_data/reference_data/chr1-hg19_genes.gtf\n", + "linux_data/genomics_data/._na12878_q20_annot.vcf\n", + "linux_data/genomics_data/na12878_q20_annot.vcf\n", + "linux_data/genomics_data/._Encode-hesc-Nanog.bed\n", + "linux_data/genomics_data/Encode-hesc-Nanog.bed\n", + "linux_data/other/._Mov10_rnaseq_metadata.txt\n", + "linux_data/other/Mov10_rnaseq_metadata.txt\n", + "linux_data/other/._sequences.fa\n", + "linux_data/other/sequences.fa\n", + "linux_data/raw_fastq/._Irrel_kd_1.subset.fq\n", + "linux_data/raw_fastq/Irrel_kd_1.subset.fq\n", + "linux_data/raw_fastq/._Mov10_oe_1.subset.fq\n", + "linux_data/raw_fastq/Mov10_oe_1.subset.fq\n", + "linux_data/raw_fastq/._Irrel_kd_3.subset.fq\n", + "linux_data/raw_fastq/Irrel_kd_3.subset.fq\n", + "linux_data/raw_fastq/._Mov10_oe_3.subset.fq\n", + "linux_data/raw_fastq/Mov10_oe_3.subset.fq\n", + "linux_data/raw_fastq/._Irrel_kd_2.subset.fq\n", + "linux_data/raw_fastq/Irrel_kd_2.subset.fq\n", + "linux_data/raw_fastq/._Mov10_oe_2.subset.fq\n", + "linux_data/raw_fastq/Mov10_oe_2.subset.fq\n" + ] + } + ], + "source": [ + "tar -xvJf linux_data.tar.xz" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Using one command list the contents of the reference_data directory that is within the linux_data directory." + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "chr1.fa chr1-hg19_genes.gtf selected_fastq\n" + ] + } + ], + "source": [ + "cd linux_data\n", + "cd reference_data\n", + "ls" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Create a new folder in `linux_data` called `selected_fastq`" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "bash: cd: linux_data: No such file or directory\n", + "mkdir: cannot create directory ‘selected_fastq’: File exists\n" + ] + }, + { + "ename": "", + "evalue": "1", + "output_type": "error", + "traceback": [] + } + ], + "source": [ + "cd linux_data\n", + "mkdir selected_fastq" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Copy over the Irrel_kd_2.subset.fq and Mov10_oe_2.subset.fq from raw_fastq to the linux_lesson/selected_fastq folder" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/home/trinleb/linux_data/reference_data\n", + "Irrel_kd_1.subset.fq Irrel_kd_3.subset.fq Mov10_oe_2.subset.fq\n", + "Irrel_kd_2.subset.fq Mov10_oe_1.subset.fq Mov10_oe_3.subset.fq\n", + "Irrel_kd_1.subset.fq Irrel_kd_3.subset.fq Mov10_oe_2.subset.fq\n", + "Irrel_kd_2.subset.fq Mov10_oe_1.subset.fq Mov10_oe_3.subset.fq\n" + ] + } + ], + "source": [ + "pwd\n", + "cd\n", + "cd linux_data\n", + "cd raw_fastq\n", + "ls\n", + "cp Irrel_kd_2.subset.fq /home/trinleb/linux_data/selected_fastq\n", + "cp Mov10_oe_2.subset.fq /home/trinleb/linux_data/selected_fastq\n", + "ls" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Rename the `selected_fastq`folder and call it `exercise1`" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [], + "source": [ + "cd\n", + "cd linux_data\n", + "mv selected_fastq exercise1" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Wildcards" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Do each of the following using a single ls command without navigating to a different directory.\n", + "\n", + "1. List all of the files in /bin that start with the letter 'c'\n", + "2. List all of the files in /bin that contain the letter 'a'\n", + "3. List all of the files in /bin that end with the letter 'o'\n", + "4. BONUS: Using one command to list all of the files in /bin that contain either 'a' or 'c'" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "ls /usr/bin/c*\n", + "ls /usr/bin/*a*\n", + "ls /usr/bin/*o\n", + "ls /usr/bin/*[ac]*" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## History\n", + "\n", + "1. Checking the output of the history command, how many commands have you typed in so far?\n", + "2. Use the up arrow key to check the command you used before history command. What is it? Does it make sense?\n", + "3. Type several random characters on the command prompt. Can you bring the cursor to the start with Ctrl + A? Next, can you bring the cursor to the end with Ctrl + E? Finally, what happens when you use Ctrl + C?\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Files\n", + "\n", + "**Do the following in the terminal**\n", + "\n", + "1. Change directories into genomics_data. You can do this using a full or relative path.\n", + "2. Use the less command to open up the file Encode-hesc-Nanog.bed.\n", + "3. Search for the string chr11; you'll see all instances in the file highlighted.\n", + "4. Staying in the less buffer, use the shortcut to get to the end of the file. \n", + "5. Exit the less buffer and come back to the command prompt.\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Searching files\n", + "\n", + "1. Using `find` command search for the sequence file `Mov10_oe_1.subset.fq`.\n", + "2. Search for the sequence CTCAATGAGCCA in Mov10_oe_1.subset.fq. How many sequences do you find?\n", + "3. If you want to search for that sequence in **all** Mov10 replicate fastq files, what command would you use?\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Searching and redirection\n", + "\n", + "How many unique exons are present on chromosome 1 using chr1-hg19_genes.gtf?\n", + "\n", + "1. Extract only the genomic coordinates of exon features\n", + "2. Subset dataset to only keep genomic coordinates\n", + "3. Remove duplicate exons\n", + "4. Count the total number of exons" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Shell scripts\n", + "\n", + "1. Write a script `listing.sh`. Add the command which prints to screen the contents of the file `Mov10_rnaseq_metadata.txt`.\n", + "2. Add an echo statement for the command, which tells the user \"This is information about the files in our dataset:\"\n", + "3. Run the new script. Report the contents of the new script and the output you got after running it." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + " ## Bash variables\n", + "\n", + "1. Use the `$file` variable as input to the head and tail commands, and modify the arguments to display only four lines from any file. \n", + "2. Create a new variable called meta and assign it the value Mov10_rnaseq_metadata.txt. For the following questions, use the $meta variable but do not change directories. Provide the code you would run to:\n", + " \n", + " a. Display the contents of the file using cat.\n", + " b. Retrieve only the lines which contain normal samples. (Hint: use grep)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + " \n", + "## Filename\n", + "\n", + "1. How would you modify basename command above to only return Mov10_oe_1 from the filename `Mov10_oe_1.subset.fq`?\n", + "2. Use basename with the file Irrel_kd_1.subset.fq as input. Return only Irrel_kd_1 to the terminal." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## `for` loop\n", + "\n", + "Write a loop to print out the number of lines in each fasta file in the dataset. The output should look something like this:\n", + "```\n", + " Irrel_kd_1.subset.fq 891684\n", + " Irrel_kd_2.subset.fq 767072\n", + " Irrel_kd_3.subset.fq 586196\n", + " Mov10_oe_1.subset.fq 1223600\n", + " Mov10_oe_2.subset.fq 1110016\n", + " Mov10_oe_3.subset.fq 690816\n", + "```" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Bash", + "language": "bash", + "name": "bash" + }, + "language_info": { + "codemirror_mode": "shell", + "file_extension": ".sh", + "mimetype": "text/x-sh", + "name": "bash" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/bash_class_assignment.ipynb b/bash_class_assignment.ipynb new file mode 100644 index 0000000..d65850a --- /dev/null +++ b/bash_class_assignment.ipynb @@ -0,0 +1,3827 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# `bash` practicals\n", + "\n", + "## Directory and file structure\n", + "\n", + "Using one command move to your home directory." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "cd" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Change your directory on your local drive (mounted from virtualbox). " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Confirm that you are in the correct location." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/home/trinleb\n" + ] + } + ], + "source": [ + "pwd" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Download the data required for the class. The files are `split` into two part because of GitHub limitation." + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "--2021-09-01 20:42:23-- https://github.com/cb2edu/CB2-101-BioComp/raw/2020/01-Linux_101/data/linux_data.tar.xz.partaa\n", + "Resolving github.com (github.com)... 140.82.113.4\n", + "Connecting to github.com (github.com)|140.82.113.4|:443... connected.\n", + "HTTP request sent, awaiting response... 302 Found\n", + "Location: https://raw.githubusercontent.com/cb2edu/CB2-101-BioComp/2020/01-Linux_101/data/linux_data.tar.xz.partaa [following]\n", + "--2021-09-01 20:42:23-- https://raw.githubusercontent.com/cb2edu/CB2-101-BioComp/2020/01-Linux_101/data/linux_data.tar.xz.partaa\n", + "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.110.133, 185.199.111.133, ...\n", + "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.\n", + "HTTP request sent, awaiting response... 200 OK\n", + "Length: 94371840 (90M) [application/octet-stream]\n", + "Saving to: ‘linux_data.tar.xz.partaa’\n", + "\n", + "100%[======================================>] 94,371,840 80.4MB/s in 1.1s \n", + "\n", + "2021-09-01 20:42:25 (80.4 MB/s) - ‘linux_data.tar.xz.partaa’ saved [94371840/94371840]\n", + "\n", + "--2021-09-01 20:42:25-- https://github.com/cb2edu/CB2-101-BioComp/raw/2020/01-Linux_101/data/linux_data.tar.xz.partab\n", + "Resolving github.com (github.com)... 140.82.113.4\n", + "Connecting to github.com (github.com)|140.82.113.4|:443... connected.\n", + "HTTP request sent, awaiting response... 302 Found\n", + "Location: https://raw.githubusercontent.com/cb2edu/CB2-101-BioComp/2020/01-Linux_101/data/linux_data.tar.xz.partab [following]\n", + "--2021-09-01 20:42:25-- https://raw.githubusercontent.com/cb2edu/CB2-101-BioComp/2020/01-Linux_101/data/linux_data.tar.xz.partab\n", + "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.110.133, 185.199.111.133, ...\n", + "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.\n", + "HTTP request sent, awaiting response... 200 OK\n", + "Length: 40809432 (39M) [application/octet-stream]\n", + "Saving to: ‘linux_data.tar.xz.partab’\n", + "\n", + "100%[======================================>] 40,809,432 74.6MB/s in 0.5s \n", + "\n", + "2021-09-01 20:42:26 (74.6 MB/s) - ‘linux_data.tar.xz.partab’ saved [40809432/40809432]\n", + "\n" + ] + } + ], + "source": [ + "wget https://github.com/cb2edu/CB2-101-BioComp/raw/2020/01-Linux_101/data/linux_data.tar.xz.partaa\n", + "wget https://github.com/cb2edu/CB2-101-BioComp/raw/2020/01-Linux_101/data/linux_data.tar.xz.partab" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Check that there are two files in the directory." + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "bash_class_assignment.ipynb linux_data\n", + "git_practicals.ipynb\t linux_data.tar.xz\n", + "igv\t\t\t linux_data.tar.xz.partaa\n", + "info302\t\t\t linux_data.tar.xz.partab\n", + "info302_assignment\t problematic_sites_sarsCov2.vcf\n" + ] + } + ], + "source": [ + "ls" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Join the parts." + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "bash_class_assignment.ipynb linux_data\n", + "git_practicals.ipynb\t linux_data.tar.xz\n", + "igv\t\t\t linux_data.tar.xz.partaa\n", + "info302\t\t\t linux_data.tar.xz.partab\n", + "info302_assignment\t problematic_sites_sarsCov2.vcf\n" + ] + } + ], + "source": [ + "cat linux_data.tar.xz.parta* > linux_data.tar.xz\n", + "ls" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We don't need the parts anymore." + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "rm linux_data.tar.xz.parta*" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Unzip the data." + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "._linux_data\n", + "linux_data/\n", + "linux_data/._raw_fastq\n", + "linux_data/raw_fastq/\n", + "linux_data/._.DS_Store\n", + "linux_data/.DS_Store\n", + "linux_data/._other\n", + "linux_data/other/\n", + "linux_data/._genomics_data\n", + "linux_data/genomics_data/\n", + "linux_data/._reference_data\n", + "linux_data/reference_data/\n", + "linux_data/._.my_hidden_directory\n", + "linux_data/.my_hidden_directory/\n", + "linux_data/.my_hidden_directory/._hidden.txt\n", + "linux_data/.my_hidden_directory/hidden.txt\n", + "linux_data/reference_data/._chr1.fa\n", + "linux_data/reference_data/chr1.fa\n", + "linux_data/reference_data/._chr1-hg19_genes.gtf\n", + "linux_data/reference_data/chr1-hg19_genes.gtf\n", + "linux_data/genomics_data/._na12878_q20_annot.vcf\n", + "linux_data/genomics_data/na12878_q20_annot.vcf\n", + "linux_data/genomics_data/._Encode-hesc-Nanog.bed\n", + "linux_data/genomics_data/Encode-hesc-Nanog.bed\n", + "linux_data/other/._Mov10_rnaseq_metadata.txt\n", + "linux_data/other/Mov10_rnaseq_metadata.txt\n", + "linux_data/other/._sequences.fa\n", + "linux_data/other/sequences.fa\n", + "linux_data/raw_fastq/._Irrel_kd_1.subset.fq\n", + "linux_data/raw_fastq/Irrel_kd_1.subset.fq\n", + "linux_data/raw_fastq/._Mov10_oe_1.subset.fq\n", + "linux_data/raw_fastq/Mov10_oe_1.subset.fq\n", + "linux_data/raw_fastq/._Irrel_kd_3.subset.fq\n", + "linux_data/raw_fastq/Irrel_kd_3.subset.fq\n", + "linux_data/raw_fastq/._Mov10_oe_3.subset.fq\n", + "linux_data/raw_fastq/Mov10_oe_3.subset.fq\n", + "linux_data/raw_fastq/._Irrel_kd_2.subset.fq\n", + "linux_data/raw_fastq/Irrel_kd_2.subset.fq\n", + "linux_data/raw_fastq/._Mov10_oe_2.subset.fq\n", + "linux_data/raw_fastq/Mov10_oe_2.subset.fq\n" + ] + } + ], + "source": [ + "tar -xvJf linux_data.tar.xz" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Using one command list the contents of the reference_data directory that is within the linux_data directory." + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "chr1.fa chr1-hg19_genes.gtf selected_fastq\n" + ] + } + ], + "source": [ + "cd linux_data\n", + "cd reference_data\n", + "ls" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Create a new folder in `linux_data` called `selected_fastq`" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "bash: cd: linux_data: No such file or directory\n", + "mkdir: cannot create directory ‘selected_fastq’: File exists\n" + ] + }, + { + "ename": "", + "evalue": "1", + "output_type": "error", + "traceback": [] + } + ], + "source": [ + "cd linux_data\n", + "mkdir selected_fastq" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Copy over the Irrel_kd_2.subset.fq and Mov10_oe_2.subset.fq from raw_fastq to the linux_lesson/selected_fastq folder" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/home/trinleb/linux_data/reference_data\n", + "Irrel_kd_1.subset.fq Irrel_kd_3.subset.fq Mov10_oe_2.subset.fq\n", + "Irrel_kd_2.subset.fq Mov10_oe_1.subset.fq Mov10_oe_3.subset.fq\n", + "Irrel_kd_1.subset.fq Irrel_kd_3.subset.fq Mov10_oe_2.subset.fq\n", + "Irrel_kd_2.subset.fq Mov10_oe_1.subset.fq Mov10_oe_3.subset.fq\n" + ] + } + ], + "source": [ + "pwd\n", + "cd\n", + "cd linux_data\n", + "cd raw_fastq\n", + "ls\n", + "cp Irrel_kd_2.subset.fq /home/trinleb/linux_data/selected_fastq\n", + "cp Mov10_oe_2.subset.fq /home/trinleb/linux_data/selected_fastq\n", + "ls" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Rename the `selected_fastq`folder and call it `exercise1`" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [], + "source": [ + "cd\n", + "cd linux_data\n", + "mv selected_fastq exercise1" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Wildcards" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Do each of the following using a single ls command without navigating to a different directory.\n", + "\n", + "1. List all of the files in /bin that start with the letter 'c'\n", + "2. List all of the files in /bin that contain the letter 'a'\n", + "3. List all of the files in /bin that end with the letter 'o'\n", + "4. BONUS: Using one command to list all of the files in /bin that contain either 'a' or 'c'" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/usr/bin/c++\t\t\t\t /usr/bin/chsh\n", + "/usr/bin/c2ph\t\t\t\t /usr/bin/chvt\n", + "/usr/bin/c89\t\t\t\t /usr/bin/ci\n", + "/usr/bin/c99\t\t\t\t /usr/bin/cifscreds\n", + "/usr/bin/cairo-sphinx\t\t\t /usr/bin/cifsdd\n", + "/usr/bin/caja\t\t\t\t /usr/bin/cifsiostat\n", + "/usr/bin/caja-autorun-software\t\t /usr/bin/cinder\n", + "/usr/bin/caja-connect-server\t\t /usr/bin/cinder-2\n", + "/usr/bin/caja-file-management-properties /usr/bin/cinder-2.7\n", + "/usr/bin/caja-sendto\t\t\t /usr/bin/ciptool\n", + "/usr/bin/cal\t\t\t\t /usr/bin/circo\n", + "/usr/bin/ca-legacy\t\t\t /usr/bin/cisco-decrypt\n", + "/usr/bin/calibrate_ppa\t\t\t /usr/bin/cksum\n", + "/usr/bin/canberra-boot\t\t\t /usr/bin/clean-binary-files\n", + "/usr/bin/canberra-gtk-play\t\t /usr/bin/clear\n", + "/usr/bin/cancel\t\t\t\t /usr/bin/clibrary\n", + "/usr/bin/cancel.cups\t\t\t /usr/bin/clibrary2\n", + "/usr/bin/captoinfo\t\t\t /usr/bin/clpi_dump\n", + "/usr/bin/cat\t\t\t\t /usr/bin/cluster\n", + "/usr/bin/catchsegv\t\t\t /usr/bin/cmp\n", + "/usr/bin/catman\t\t\t\t /usr/bin/cmsutil\n", + "/usr/bin/cc\t\t\t\t /usr/bin/cmtime\n", + "/usr/bin/ccomps\t\t\t\t /usr/bin/co\n", + "/usr/bin/cd\t\t\t\t /usr/bin/col\n", + "/usr/bin/cd-create-profile\t\t /usr/bin/colcrt\n", + "/usr/bin/cdda2ogg\t\t\t /usr/bin/collectl\n", + "/usr/bin/cdda2wav\t\t\t /usr/bin/colmux\n", + "/usr/bin/cdda-player\t\t\t /usr/bin/colormgr\n", + "/usr/bin/cd-drive\t\t\t /usr/bin/colrm\n", + "/usr/bin/cd-fix-profile\t\t\t /usr/bin/column\n", + "/usr/bin/cd-iccdump\t\t\t /usr/bin/combinedeltarpm\n", + "/usr/bin/cd-info\t\t\t /usr/bin/combinediff\n", + "/usr/bin/cd-it8\t\t\t\t /usr/bin/comm\n", + "/usr/bin/cdparanoia\t\t\t /usr/bin/command\n", + "/usr/bin/cd-paranoia\t\t\t /usr/bin/compare\n", + "/usr/bin/cdrdao\t\t\t\t /usr/bin/compile_et\n", + "/usr/bin/cd-read\t\t\t /usr/bin/composite\n", + "/usr/bin/cdrecord\t\t\t /usr/bin/compress\n", + "/usr/bin/celtdec051\t\t\t /usr/bin/conjure\n", + "/usr/bin/celtenc051\t\t\t /usr/bin/connection_recovery\n", + "/usr/bin/centrino-decode\t\t /usr/bin/consolehelper\n", + "/usr/bin/certmaster-getcert\t\t /usr/bin/consolehelper-gtk\n", + "/usr/bin/certtool\t\t\t /usr/bin/convert\n", + "/usr/bin/certutil\t\t\t /usr/bin/coredumpctl\n", + "/usr/bin/cfadmin\t\t\t /usr/bin/coverage\n", + "/usr/bin/c++filt\t\t\t /usr/bin/coverage2\n", + "/usr/bin/cgclassify\t\t\t /usr/bin/coverage-2.7\n", + "/usr/bin/cgcreate\t\t\t /usr/bin/cp\n", + "/usr/bin/cgdelete\t\t\t /usr/bin/cpan\n", + "/usr/bin/cgexec\t\t\t\t /usr/bin/cpio\n", + "/usr/bin/cgget\t\t\t\t /usr/bin/cpp\n", + "/usr/bin/cgset\t\t\t\t /usr/bin/cpupower\n", + "/usr/bin/cgsnapshot\t\t\t /usr/bin/cq\n", + "/usr/bin/chacl\t\t\t\t /usr/bin/create-jar-links\n", + "/usr/bin/chage\t\t\t\t /usr/bin/createrepo\n", + "/usr/bin/chardetect\t\t\t /usr/bin/crlutil\n", + "/usr/bin/charmap\t\t\t /usr/bin/crontab\n", + "/usr/bin/chattr\t\t\t\t /usr/bin/crywrap\n", + "/usr/bin/chcat\t\t\t\t /usr/bin/cscope\n", + "/usr/bin/chcon\t\t\t\t /usr/bin/cscope-indexer\n", + "/usr/bin/check-binary-files\t\t /usr/bin/csh\n", + "/usr/bin/checkisomd5\t\t\t /usr/bin/csplit\n", + "/usr/bin/check_mk_agent\t\t\t /usr/bin/csslint-0.6\n", + "/usr/bin/check_mk_caching_agent\t\t /usr/bin/ctags\n", + "/usr/bin/checkmodule\t\t\t /usr/bin/cue2toc\n", + "/usr/bin/checkpolicy\t\t\t /usr/bin/cups-calibrate\n", + "/usr/bin/checksctp\t\t\t /usr/bin/cupstestdsc\n", + "/usr/bin/cheese\t\t\t\t /usr/bin/cupstestppd\n", + "/usr/bin/chfn\t\t\t\t /usr/bin/curl\n", + "/usr/bin/chgrp\t\t\t\t /usr/bin/cut\n", + "/usr/bin/chmem\t\t\t\t /usr/bin/cvt\n", + "/usr/bin/chmod\t\t\t\t /usr/bin/cvtsudoers\n", + "/usr/bin/chown\t\t\t\t /usr/bin/cwutil\n", + "/usr/bin/chrt\n", + "/usr/bin/7za\n", + "/usr/bin/a2p\n", + "/usr/bin/abrt-action-analyze-backtrace\n", + "/usr/bin/abrt-action-analyze-c\n", + "/usr/bin/abrt-action-analyze-ccpp-local\n", + "/usr/bin/abrt-action-analyze-core\n", + "/usr/bin/abrt-action-analyze-java\n", + "/usr/bin/abrt-action-analyze-oops\n", + "/usr/bin/abrt-action-analyze-python\n", + "/usr/bin/abrt-action-analyze-vmcore\n", + "/usr/bin/abrt-action-analyze-vulnerability\n", + "/usr/bin/abrt-action-analyze-xorg\n", + "/usr/bin/abrt-action-check-oops-for-hw-error\n", + "/usr/bin/abrt-action-generate-backtrace\n", + "/usr/bin/abrt-action-generate-core-backtrace\n", + "/usr/bin/abrt-action-install-debuginfo\n", + "/usr/bin/abrt-action-list-dsos\n", + "/usr/bin/abrt-action-notify\n", + "/usr/bin/abrt-action-perform-ccpp-analysis\n", + "/usr/bin/abrt-action-save-kernel-data\n", + "/usr/bin/abrt-action-save-package-data\n", + "/usr/bin/abrt-action-trim-files\n", + "/usr/bin/abrt-applet\n", + "/usr/bin/abrt-cli\n", + "/usr/bin/abrt-dump-oops\n", + "/usr/bin/abrt-dump-xorg\n", + "/usr/bin/abrt-handle-upload\n", + "/usr/bin/abrt-merge-pstoreoops\n", + "/usr/bin/abrt-watch-log\n", + "/usr/bin/abs2rel\n", + "/usr/bin/ac\n", + "/usr/bin/aclocal\n", + "/usr/bin/aclocal-1.13\n", + "/usr/bin/aconnect\n", + "/usr/bin/acyclic\n", + "/usr/bin/addr2line\n", + "/usr/bin/afm2tfm\n", + "/usr/bin/afs5log\n", + "/usr/bin/agentxtrap\n", + "/usr/bin/alias\n", + "/usr/bin/allcm\n", + "/usr/bin/allec\n", + "/usr/bin/allneeded\n", + "/usr/bin/alsabat\n", + "/usr/bin/alsa-delay\n", + "/usr/bin/alsaloop\n", + "/usr/bin/alsamixer\n", + "/usr/bin/alsatplg\n", + "/usr/bin/alsaucm\n", + "/usr/bin/alsaunmute\n", + "/usr/bin/alt-java\n", + "/usr/bin/amidi\n", + "/usr/bin/amixer\n", + "/usr/bin/amstex\n", + "/usr/bin/amuFormat.sh\n", + "/usr/bin/animate\n", + "/usr/bin/aplay\n", + "/usr/bin/aplaymidi\n", + "/usr/bin/apm\n", + "/usr/bin/applydeltarpm\n", + "/usr/bin/appstream-compose\n", + "/usr/bin/appstream-util\n", + "/usr/bin/apropos\n", + "/usr/bin/ar\n", + "/usr/bin/arch\n", + "/usr/bin/arecord\n", + "/usr/bin/arecordmidi\n", + "/usr/bin/arpaname\n", + "/usr/bin/as\n", + "/usr/bin/asadmin\n", + "/usr/bin/ascii-xfr\n", + "/usr/bin/aseqdump\n", + "/usr/bin/aseqnet\n", + "/usr/bin/aserver\n", + "/usr/bin/at\n", + "/usr/bin/atom\n", + "/usr/bin/atq\n", + "/usr/bin/atril\n", + "/usr/bin/atril-previewer\n", + "/usr/bin/atril-thumbnailer\n", + "/usr/bin/atrm\n", + "/usr/bin/attr\n", + "/usr/bin/audit2allow\n", + "/usr/bin/audit2why\n", + "/usr/bin/auditbeat\n", + "/usr/bin/aulast\n", + "/usr/bin/aulastlog\n", + "/usr/bin/ausyscall\n", + "/usr/bin/autoconf\n", + "/usr/bin/autoexpect\n", + "/usr/bin/autoheader\n", + "/usr/bin/autom4te\n", + "/usr/bin/automake\n", + "/usr/bin/automake-1.13\n", + "/usr/bin/autopoint\n", + "/usr/bin/autoreconf\n", + "/usr/bin/autoscan\n", + "/usr/bin/autoupdate\n", + "/usr/bin/auvirt\n", + "/usr/bin/awk\n", + "/usr/bin/axfer\n", + "/usr/bin/baobab\n", + "/usr/bin/base64\n", + "/usr/bin/basename\n", + "/usr/bin/bash\n", + "/usr/bin/bashbug\n", + "/usr/bin/bashbug-64\n", + "/usr/bin/batch\n", + "/usr/bin/bdftruncate\n", + "/usr/bin/blkparse\n", + "/usr/bin/blkrawverify\n", + "/usr/bin/blktrace\n", + "/usr/bin/bond2team\n", + "/usr/bin/brasero\n", + "/usr/bin/brltty-install\n", + "/usr/bin/btattach\n", + "/usr/bin/btrace\n", + "/usr/bin/btreplay\n", + "/usr/bin/build-classpath\n", + "/usr/bin/build-classpath-directory\n", + "/usr/bin/build-jar-repository\n", + "/usr/bin/bundle_image\n", + "/usr/bin/byacc\n", + "/usr/bin/byobu-ctrl-a\n", + "/usr/bin/byobu-disable\n", + "/usr/bin/byobu-disable-prompt\n", + "/usr/bin/byobu-enable\n", + "/usr/bin/byobu-enable-prompt\n", + "/usr/bin/byobu-janitor\n", + "/usr/bin/byobu-launch\n", + "/usr/bin/byobu-launcher\n", + "/usr/bin/byobu-launcher-install\n", + "/usr/bin/byobu-launcher-uninstall\n", + "/usr/bin/byobu-layout\n", + "/usr/bin/byobu-select-backend\n", + "/usr/bin/byobu-status\n", + "/usr/bin/byobu-status-detail\n", + "/usr/bin/byobu-ugraph\n", + "/usr/bin/bzcat\n", + "/usr/bin/cairo-sphinx\n", + "/usr/bin/caja\n", + "/usr/bin/caja-autorun-software\n", + "/usr/bin/caja-connect-server\n", + "/usr/bin/caja-file-management-properties\n", + "/usr/bin/caja-sendto\n", + "/usr/bin/cal\n", + "/usr/bin/ca-legacy\n", + "/usr/bin/calibrate_ppa\n", + "/usr/bin/canberra-boot\n", + "/usr/bin/canberra-gtk-play\n", + "/usr/bin/cancel\n", + "/usr/bin/cancel.cups\n", + "/usr/bin/captoinfo\n", + "/usr/bin/cat\n", + "/usr/bin/catchsegv\n", + "/usr/bin/catman\n", + "/usr/bin/cd-create-profile\n", + "/usr/bin/cdda2ogg\n", + "/usr/bin/cdda2wav\n", + "/usr/bin/cdda-player\n", + "/usr/bin/cdparanoia\n", + "/usr/bin/cd-paranoia\n", + "/usr/bin/cdrdao\n", + "/usr/bin/cd-read\n", + "/usr/bin/certmaster-getcert\n", + "/usr/bin/cfadmin\n", + "/usr/bin/cgclassify\n", + "/usr/bin/cgcreate\n", + "/usr/bin/cgsnapshot\n", + "/usr/bin/chacl\n", + "/usr/bin/chage\n", + "/usr/bin/chardetect\n", + "/usr/bin/charmap\n", + "/usr/bin/chattr\n", + "/usr/bin/chcat\n", + "/usr/bin/check-binary-files\n", + "/usr/bin/check_mk_agent\n", + "/usr/bin/check_mk_caching_agent\n", + "/usr/bin/cifsiostat\n", + "/usr/bin/clean-binary-files\n", + "/usr/bin/clear\n", + "/usr/bin/clibrary\n", + "/usr/bin/clibrary2\n", + "/usr/bin/combinedeltarpm\n", + "/usr/bin/command\n", + "/usr/bin/compare\n", + "/usr/bin/ControlPanel\n", + "/usr/bin/coverage\n", + "/usr/bin/coverage2\n", + "/usr/bin/coverage-2.7\n", + "/usr/bin/cpan\n", + "/usr/bin/create-jar-links\n", + "/usr/bin/createrepo\n", + "/usr/bin/crontab\n", + "/usr/bin/crywrap\n", + "/usr/bin/ctags\n", + "/usr/bin/cups-calibrate\n", + "/usr/bin/danetool\n", + "/usr/bin/dapltest\n", + "/usr/bin/date\n", + "/usr/bin/db_archive\n", + "/usr/bin/db_deadlock\n", + "/usr/bin/db_hotbackup\n", + "/usr/bin/db_load\n", + "/usr/bin/db_replicate\n", + "/usr/bin/db_stat\n", + "/usr/bin/db_upgrade\n", + "/usr/bin/dbus-cleanup-sockets\n", + "/usr/bin/dbus-daemon\n", + "/usr/bin/dbus-launch\n", + "/usr/bin/dbus-update-activation-environment\n", + "/usr/bin/dbwrap_tool\n", + "/usr/bin/deallocvt\n", + "/usr/bin/debuginfo-install\n", + "/usr/bin/desktop-file-install\n", + "/usr/bin/desktop-file-validate\n", + "/usr/bin/detect_ppa\n", + "/usr/bin/dgawk\n", + "/usr/bin/diff-jars\n", + "/usr/bin/diffstat\n", + "/usr/bin/dijkstra\n", + "/usr/bin/dimax_init\n", + "/usr/bin/dirname\n", + "/usr/bin/dislocate\n", + "/usr/bin/display\n", + "/usr/bin/dnsdomainname\n", + "/usr/bin/domainname\n", + "/usr/bin/dracut\n", + "/usr/bin/dtrace\n", + "/usr/bin/dvd-ram-control\n", + "/usr/bin/dvd+rw-format\n", + "/usr/bin/dvd+rw-mediainfo\n", + "/usr/bin/dvi2fax\n", + "/usr/bin/dvilualatex\n", + "/usr/bin/dviluatex\n", + "/usr/bin/dynamodb_dump\n", + "/usr/bin/dynamodb_load\n", + "/usr/bin/easy_install\n", + "/usr/bin/easy_install-2.7\n", + "/usr/bin/easy_install-3.6\n", + "/usr/bin/elbadmin\n", + "/usr/bin/emacs\n", + "/usr/bin/emacs-24.3\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/usr/bin/emacs-24.3-nox\n", + "/usr/bin/emacsclient\n", + "/usr/bin/empathy\n", + "/usr/bin/empathy-accounts\n", + "/usr/bin/empathy-debugger\n", + "/usr/bin/enchant\n", + "/usr/bin/enchant-lsmod\n", + "/usr/bin/engrampa\n", + "/usr/bin/espeak\n", + "/usr/bin/etags\n", + "/usr/bin/etags.emacs\n", + "/usr/bin/eu-addr2line\n", + "/usr/bin/eu-ar\n", + "/usr/bin/eu-make-debug-archive\n", + "/usr/bin/eu-ranlib\n", + "/usr/bin/eu-readelf\n", + "/usr/bin/eu-stack\n", + "/usr/bin/evince-thumbnailer\n", + "/usr/bin/exo-preferred-applications\n", + "/usr/bin/expand\n", + "/usr/bin/extractbb\n", + "/usr/bin/factor\n", + "/usr/bin/fail2ban-client\n", + "/usr/bin/fail2ban-python\n", + "/usr/bin/fail2ban-regex\n", + "/usr/bin/fail2ban-server\n", + "/usr/bin/fallocate\n", + "/usr/bin/false\n", + "/usr/bin/fc-cache\n", + "/usr/bin/fc-cache-32\n", + "/usr/bin/fc-cache-64\n", + "/usr/bin/fc-cat\n", + "/usr/bin/fc-match\n", + "/usr/bin/fc-pattern\n", + "/usr/bin/fc-scan\n", + 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"/usr/bin/mformat\n", + "/usr/bin/mfplain\n", + "/usr/bin/mft_uninstall.sh\n", + "/usr/bin/mib2c-update\n", + "/usr/bin/migratepages\n", + "/usr/bin/mixartloader\n", + "/usr/bin/mkafmmap\n", + "/usr/bin/mkfontscale\n", + "/usr/bin/mkluatexfontdb\n", + "/usr/bin/mkmanifest\n", + "/usr/bin/mkpasswd\n", + "/usr/bin/mlabel\n", + "/usr/bin/mlnx_dump_parser\n", + "/usr/bin/mlnx_interface_mgr.sh\n", + "/usr/bin/mlxcables\n", + "/usr/bin/mlxcables_ext\n", + "/usr/bin/mlx_fpga\n", + "/usr/bin/mlx_fpga_ext\n", + "/usr/bin/mlxfwmanager\n", + "/usr/bin/mlxgearbox\n", + "/usr/bin/mlxtrace\n", + "/usr/bin/mlxtrace_ext\n", + "/usr/bin/montage\n", + "/usr/bin/mousetweaks\n", + "/usr/bin/mpartition\n", + "/usr/bin/mpaste\n", + "/usr/bin/mpstat\n", + "/usr/bin/msgattrib\n", + "/usr/bin/msgcat\n", + "/usr/bin/msghack\n", + "/usr/bin/mshortname\n", + "/usr/bin/mshowfat\n", + "/usr/bin/mstarchive\n", + "/usr/bin/mst_cable\n", + "/usr/bin/mstfwmanager\n" + ] + }, + { + "name": "stdout", + "output_type": 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"/usr/bin/pyrsa-sign-2\n", + "/usr/bin/pyrsa-verify\n", + "/usr/bin/pyrsa-verify-2\n", + "/usr/bin/qemu-ga\n", + "/usr/bin/qlalr\n", + "/usr/bin/qmake-qt5\n", + "/usr/bin/quota\n", + "/usr/bin/quotasync\n", + "/usr/bin/rackup\n", + "/usr/bin/rake\n", + "/usr/bin/ranlib\n", + "/usr/bin/rapper\n", + "/usr/bin/rarian-example\n", + "/usr/bin/rarian-sk-config\n", + "/usr/bin/rarian-sk-extract\n", + "/usr/bin/rarian-sk-gen-uuid\n", + "/usr/bin/rarian-sk-get-cl\n", + "/usr/bin/rarian-sk-get-content-list\n", + "/usr/bin/rarian-sk-get-extended-content-list\n", + "/usr/bin/rarian-sk-get-scripts\n", + "/usr/bin/rarian-sk-install\n", + "/usr/bin/rarian-sk-migrate\n", + "/usr/bin/rarian-sk-preinstall\n", + "/usr/bin/rarian-sk-rebuild\n", + "/usr/bin/rarian-sk-update\n", + "/usr/bin/raw\n", + "/usr/bin/raw_ethernet_burst_lat\n", + "/usr/bin/raw_ethernet_bw\n", + "/usr/bin/raw_ethernet_fs_rate\n", + "/usr/bin/raw_ethernet_lat\n", + "/usr/bin/rcsclean\n", + "/usr/bin/rdate\n", + "/usr/bin/rdma_client\n", + "/usr/bin/rdma_server\n", + "/usr/bin/rdma_xclient\n", + "/usr/bin/rdma_xserver\n", + "/usr/bin/read\n", + "/usr/bin/readcd\n", + "/usr/bin/readelf\n", + "/usr/bin/readlink\n", + "/usr/bin/readmult\n", + "/usr/bin/readom\n", + "/usr/bin/realpath\n", + "/usr/bin/rebuild-jar-repository\n", + "/usr/bin/recode-sr-latin\n", + "/usr/bin/redhat_lsb_init\n", + "/usr/bin/redhat-support-tool\n", + "/usr/bin/redland-db-upgrade\n", + "/usr/bin/regpatch\n", + "/usr/bin/rename\n", + "/usr/bin/repo-graph\n", + "/usr/bin/repomanage\n", + "/usr/bin/reporter-bugzilla\n", + "/usr/bin/reporter-mailx\n", + "/usr/bin/reporter-upload\n", + "/usr/bin/repotrack\n", + "/usr/bin/rescan-scsi-bus.sh\n", + "/usr/bin/riostream\n", + "/usr/bin/rmail\n", + "/usr/bin/rmail.postfix\n", + "/usr/bin/rnano\n", + "/usr/bin/rpmdumpheader\n", + "/usr/bin/rpmgraph\n", + "/usr/bin/rstream\n", + "/usr/bin/rumakeindex\n", + "/usr/bin/run-parts\n", + "/usr/bin/run_perftest_loopback\n", + "/usr/bin/sadf\n", + "/usr/bin/samba-regedit\n", + "/usr/bin/sandbox\n", + "/usr/bin/sane-find-scanner\n", + "/usr/bin/sar\n", + "/usr/bin/sas_disk_blink\n", + "/usr/bin/satyr\n", + "/usr/bin/saytime\n", + "/usr/bin/scanimage\n", + "/usr/bin/sccmap\n", + "/usr/bin/scl_enabled\n", + "/usr/bin/scriptreplay\n", + "/usr/bin/scrollkeeper-extract\n", + "/usr/bin/scrollkeeper-get-index-from-docpath\n", + "/usr/bin/scrollkeeper-get-toc-from-docpath\n", + "/usr/bin/scrollkeeper-install\n", + "/usr/bin/scrollkeeper-preinstall\n", + "/usr/bin/scrollkeeper-uninstall\n", + "/usr/bin/scrollkeeper-update\n", + "/usr/bin/scsi_mandat\n", + "/usr/bin/scsi_readcap\n", + "/usr/bin/scsi_ready\n", + "/usr/bin/scsi-rescan\n", + "/usr/bin/scsi_satl\n", + "/usr/bin/scsi_start\n", + "/usr/bin/scsi_temperature\n", + "/usr/bin/sctp_darn\n", + "/usr/bin/sctp_status\n", + "/usr/bin/sdbadmin\n", + "/usr/bin/sdparm\n", + "/usr/bin/sdp_long_message\n", + "/usr/bin/seahorse\n", + "/usr/bin/sealert\n", + "/usr/bin/seapplet\n", + "/usr/bin/semodule_package\n", + "/usr/bin/setarch\n", + "/usr/bin/setcifsacl\n", + "/usr/bin/setfacl\n", + "/usr/bin/setfattr\n", + "/usr/bin/setmetamode\n", + "/usr/bin/setserial\n", + "/usr/bin/setxkbmap\n", + "/usr/bin/sg_compare_and_write\n", + "/usr/bin/sg_emc_trespass\n", + "/usr/bin/sg_format\n", + "/usr/bin/sg_get_lba_status\n", + "/usr/bin/sg_map\n", + "/usr/bin/sg_map26\n", + "/usr/bin/sg_raw\n", + "/usr/bin/sg_rdac\n", + "/usr/bin/sg_read\n", + "/usr/bin/sg_read_block_limits\n", + "/usr/bin/sg_read_buffer\n", + "/usr/bin/sg_readcap\n", + "/usr/bin/sg_read_long\n", + "/usr/bin/sg_reassign\n", + "/usr/bin/sg_referrals\n", + "/usr/bin/sg_safte\n", + "/usr/bin/sg_sanitize\n", + "/usr/bin/sg_sat_identify\n", + "/usr/bin/sg_sat_phy_event\n", + "/usr/bin/sg_sat_set_features\n", + "/usr/bin/sg_scan\n", + "/usr/bin/sg_senddiag\n", + "/usr/bin/sg_start\n", + "/usr/bin/sg_unmap\n", + "/usr/bin/sg_write_same\n", + "/usr/bin/sha1sum\n", + "/usr/bin/sha224sum\n", + "/usr/bin/sha256sum\n", + "/usr/bin/sha384sum\n", + "/usr/bin/sha512sum\n", + "/usr/bin/sharesec\n", + "/usr/bin/shasum\n", + "/usr/bin/show-changed-rco\n", + "/usr/bin/show-installed\n", + "/usr/bin/simple-scan\n", + "/usr/bin/slabtop\n", + "/usr/bin/smbcacls\n", + "/usr/bin/smbcquotas\n", + "/usr/bin/smbpasswd\n", + "/usr/bin/smbtar\n", + "/usr/bin/sndfile-resample\n", + "/usr/bin/spax\n", + "/usr/bin/spd-say\n", + "/usr/bin/speaker-test\n", + "/usr/bin/speech-dispatcher\n", + "/usr/bin/spice-vdagent\n", + "/usr/bin/splain\n", + "/usr/bin/ssh-add\n", + "/usr/bin/ssh-agent\n", + "/usr/bin/ssh-keyscan\n", + "/usr/bin/sshpass\n", + "/usr/bin/ssltap\n", + "/usr/bin/sss_ssh_authorizedkeys\n", + "/usr/bin/stap\n", + "/usr/bin/stapbpf\n", + "/usr/bin/stapdyn\n", + "/usr/bin/stap-merge\n", + "/usr/bin/stap-prep\n", + "/usr/bin/stap-report\n", + "/usr/bin/staprun\n", + "/usr/bin/stapsh\n", + "/usr/bin/start-pulseaudio-x11\n", + "/usr/bin/startx\n", + "/usr/bin/startxfce4\n", + "/usr/bin/stat\n", + "/usr/bin/states\n", + "/usr/bin/strace\n", + "/usr/bin/strace-log-merge\n", + "/usr/bin/stream\n", + "/usr/bin/subscription-manager\n", + "/usr/bin/sudoreplay\n", + "/usr/bin/svnadmin\n", + "/usr/bin/syndaemon\n", + "/usr/bin/system-config-abrt\n", + "/usr/bin/system-config-date\n", + "/usr/bin/system-config-language\n", + "/usr/bin/system-config-printer-applet\n", + "/usr/bin/systemd-analyze\n", + "/usr/bin/systemd-ask-password\n", + "/usr/bin/systemd-cat\n", + "/usr/bin/systemd-delta\n", + "/usr/bin/systemd-escape\n", + "/usr/bin/systemd-machine-id-setup\n", + "/usr/bin/systemd-nspawn\n", + "/usr/bin/systemd-path\n", + "/usr/bin/systemd-tty-ask-password-agent\n", + "/usr/bin/tabs\n", + "/usr/bin/tac\n", + "/usr/bin/tail\n", + "/usr/bin/tailf\n", + "/usr/bin/tapestat\n", + "/usr/bin/tar\n", + "/usr/bin/targetcli\n", + "/usr/bin/targetclid\n", + "/usr/bin/targetctl\n", + "/usr/bin/taskadmin\n", + "/usr/bin/taskset\n", + "/usr/bin/tcptraceroute\n", + "/usr/bin/tc_wrap.py\n", + "/usr/bin/teamd\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/usr/bin/teamdctl\n", + "/usr/bin/teamnl\n", + "/usr/bin/telepathy-gabble-xmpp-console\n", + "/usr/bin/testlibraw\n", + "/usr/bin/testparm\n", + "/usr/bin/test_ppa\n", + "/usr/bin/texconfig-dialog\n", + "/usr/bin/texhash\n", + "/usr/bin/texi2any\n", + "/usr/bin/texlua\n", + "/usr/bin/texluac\n", + "/usr/bin/text2wave\n", + "/usr/bin/thunar\n", + "/usr/bin/Thunar\n", + "/usr/bin/thunar-settings\n", + "/usr/bin/thunar-volman\n", + "/usr/bin/thunar-volman-settings\n", + "/usr/bin/timedatectl\n", + "/usr/bin/timed-read\n", + "/usr/bin/tload\n", + "/usr/bin/tnameserv\n", + "/usr/bin/totem-video-thumbnailer\n", + "/usr/bin/tracepath\n", + "/usr/bin/tracepath6\n", + "/usr/bin/traceroute\n", + "/usr/bin/traceroute6\n", + "/usr/bin/tracker\n", + "/usr/bin/transmission-create\n", + "/usr/bin/transmission-edit\n", + "/usr/bin/transmission-gtk\n", + "/usr/bin/transmission-remote\n", + "/usr/bin/transmission-show\n", + "/usr/bin/traptoemail\n", + "/usr/bin/truncate\n", + "/usr/bin/turbostat\n", + "/usr/bin/ucmatose\n", + "/usr/bin/ucs2any\n", + "/usr/bin/ucx_read_profile\n", + "/usr/bin/udaddy\n", + "/usr/bin/udevadm\n", + "/usr/bin/umask\n", + "/usr/bin/unalias\n", + "/usr/bin/uname\n", + "/usr/bin/unexpand\n", + "/usr/bin/unflatten\n", + "/usr/bin/unicode_start\n", + "/usr/bin/unix2mac\n", + "/usr/bin/unpack200\n", + "/usr/bin/unshare\n", + "/usr/bin/unwrapdiff\n", + "/usr/bin/update-ca-trust\n", + "/usr/bin/updatedb\n", + "/usr/bin/update-desktop-database\n", + "/usr/bin/update-gtk-immodules\n", + "/usr/bin/update-mime-database\n", + "/usr/bin/updmap\n", + "/usr/bin/updmap-sys\n", + "/usr/bin/urlgrabber\n", + "/usr/bin/userformat\n", + "/usr/bin/userpasswd\n", + "/usr/bin/usx2yloader\n", + "/usr/bin/verify_blkparse\n", + "/usr/bin/vinagre\n", + "/usr/bin/virt-host-validate\n", + "/usr/bin/virt-pki-validate\n", + "/usr/bin/virt-xml-validate\n", + "/usr/bin/vmstat\n", + "/usr/bin/vmware-checkvm\n", + "/usr/bin/vmware-hgfsclient\n", + "/usr/bin/vmware-namespace-cmd\n", + "/usr/bin/vmware-rpctool\n", + "/usr/bin/vmware-toolbox-cmd\n", + "/usr/bin/vmware-user\n", + "/usr/bin/vmware-user-suid-wrapper\n", + "/usr/bin/vmware-vgauth-cmd\n", + "/usr/bin/vmware-vmblock-fuse\n", + "/usr/bin/vmware-xferlogs\n", + "/usr/bin/vxloader\n", + "/usr/bin/wait\n", + "/usr/bin/waitmax\n", + "/usr/bin/wall\n", + "/usr/bin/watch\n", + "/usr/bin/watchgnupg\n", + "/usr/bin/wavpack\n", + "/usr/bin/weather\n", + "/usr/bin/whatis\n", + "/usr/bin/whiptail\n", + "/usr/bin/whoami\n", + "/usr/bin/wvdial\n", + "/usr/bin/wvdialconf\n", + "/usr/bin/wvgain\n", + "/usr/bin/wvunpack\n", + "/usr/bin/x86_64-redhat-linux-c++\n", + "/usr/bin/x86_64-redhat-linux-g++\n", + "/usr/bin/x86_64-redhat-linux-gcc\n", + "/usr/bin/xargs\n", + "/usr/bin/xauth\n", + "/usr/bin/xbrlapi\n", + "/usr/bin/xchat\n", + "/usr/bin/xdg-email\n", + "/usr/bin/xdg-screensaver\n", + "/usr/bin/xdg-user-dirs-gtk-update\n", + "/usr/bin/xdg-user-dirs-update\n", + "/usr/bin/xdvi-xaw\n", + "/usr/bin/xelatex\n", + "/usr/bin/xfce4-accessibility-settings\n", + "/usr/bin/xfce4-appearance-settings\n", + "/usr/bin/xfce4-appfinder\n", + "/usr/bin/xfce4-display-settings\n", + "/usr/bin/xfce4-keyboard-settings\n", + "/usr/bin/xfce4-panel\n", + "/usr/bin/xfce4-popup-applicationsmenu\n", + "/usr/bin/xfce4-power-manager\n", + "/usr/bin/xfce4-power-manager-settings\n", + "/usr/bin/xfce4-settings-manager\n", + "/usr/bin/xfce4-terminal\n", + "/usr/bin/xfwm4-tweaks-settings\n", + "/usr/bin/xfwm4-workspace-settings\n", + "/usr/bin/xgamma\n", + "/usr/bin/xlsatoms\n", + "/usr/bin/xmlcatalog\n", + "/usr/bin/xmodmap\n", + "/usr/bin/xorg-x11-fonts-update-dirs\n", + "/usr/bin/xrandr\n", + "/usr/bin/xsetwacom\n", + "/usr/bin/xstdcmap\n", + "/usr/bin/xvattr\n", + "/usr/bin/xzcat\n", + "/usr/bin/yacc\n", + "/usr/bin/ypdomainname\n", + "/usr/bin/yum-config-manager\n", + "/usr/bin/yumdownloader\n", + "/usr/bin/yum-groups-manager\n", + "/usr/bin/zcat\n", + "/usr/bin/zipcloak\n", + "/usr/bin/zipdetails\n", + "/usr/bin/abrt-action-install-debuginfo\t/usr/bin/mlxmdio\n", + "/usr/bin/bd_info\t\t\t/usr/bin/modifyrepo\n", + "/usr/bin/bluetooth-sendto\t\t/usr/bin/mozo\n", + "/usr/bin/brasero\t\t\t/usr/bin/nano\n", + "/usr/bin/caja-sendto\t\t\t/usr/bin/nautilus-sendto\n", + "/usr/bin/captoinfo\t\t\t/usr/bin/neato\n", + "/usr/bin/cd-info\t\t\t/usr/bin/numademo\n", + "/usr/bin/cdrdao\t\t\t\t/usr/bin/ofed_info\n", + "/usr/bin/circo\t\t\t\t/usr/bin/ofed_rpm_info\n", + "/usr/bin/co\t\t\t\t/usr/bin/ogginfo\n", + "/usr/bin/cpio\t\t\t\t/usr/bin/papi_mem_info\n", + "/usr/bin/createrepo\t\t\t/usr/bin/papi_xml_event_info\n", + "/usr/bin/dumpiso\t\t\t/usr/bin/pdfinfo\n", + "/usr/bin/dvd+rw-mediainfo\t\t/usr/bin/pdftocairo\n", + "/usr/bin/echo\t\t\t\t/usr/bin/pinfo\n", + "/usr/bin/fuseiso\t\t\t/usr/bin/ppdpo\n", + "/usr/bin/gio\t\t\t\t/usr/bin/pulseaudio\n", + "/usr/bin/glxinfo\t\t\t/usr/bin/pygtk-demo\n", + "/usr/bin/gvfs-info\t\t\t/usr/bin/qemu-io\n", + "/usr/bin/hesinfo\t\t\t/usr/bin/rhino\n", + "/usr/bin/hwloc-info\t\t\t/usr/bin/rnano\n", + "/usr/bin/ibv_devinfo\t\t\t/usr/bin/rpm2cpio\n", + "/usr/bin/ibv_polldcinfo\t\t\t/usr/bin/sbcinfo\n", + "/usr/bin/info\t\t\t\t/usr/bin/sendiso\n", + "/usr/bin/isoinfo\t\t\t/usr/bin/sginfo\n", + "/usr/bin/iso-info\t\t\t/usr/bin/show-changed-rco\n", + "/usr/bin/kbdinfo\t\t\t/usr/bin/sudo\n", + "/usr/bin/kvno\t\t\t\t/usr/bin/ucx_info\n", + "/usr/bin/lessecho\t\t\t/usr/bin/userinfo\n", + "/usr/bin/lneato\t\t\t\t/usr/bin/who\n", + "/usr/bin/makeinfo\t\t\t/usr/bin/xdpyinfo\n", + "/usr/bin/marco\t\t\t\t/usr/bin/xdriinfo\n", + "/usr/bin/mdevices_info\t\t\t/usr/bin/xvinfo\n", + "/usr/bin/mergerepo\t\t\t/usr/bin/xwininfo\n", + "/usr/bin/minfo\t\t\t\t/usr/bin/zipinfo\n", + "/usr/bin/mkfifo\n", + "/usr/bin/7za\n", + "/usr/bin/a2p\n", + "/usr/bin/abrt-action-analyze-backtrace\n", + "/usr/bin/abrt-action-analyze-c\n", + "/usr/bin/abrt-action-analyze-ccpp-local\n", + "/usr/bin/abrt-action-analyze-core\n", + "/usr/bin/abrt-action-analyze-java\n", + "/usr/bin/abrt-action-analyze-oops\n", + "/usr/bin/abrt-action-analyze-python\n", + "/usr/bin/abrt-action-analyze-vmcore\n", + "/usr/bin/abrt-action-analyze-vulnerability\n", + "/usr/bin/abrt-action-analyze-xorg\n", + "/usr/bin/abrt-action-check-oops-for-hw-error\n", + "/usr/bin/abrt-action-generate-backtrace\n", + "/usr/bin/abrt-action-generate-core-backtrace\n", + "/usr/bin/abrt-action-install-debuginfo\n", + "/usr/bin/abrt-action-list-dsos\n", + "/usr/bin/abrt-action-notify\n", + "/usr/bin/abrt-action-perform-ccpp-analysis\n", + "/usr/bin/abrt-action-save-kernel-data\n", + "/usr/bin/abrt-action-save-package-data\n", + "/usr/bin/abrt-action-trim-files\n", + "/usr/bin/abrt-applet\n", + "/usr/bin/abrt-cli\n", + "/usr/bin/abrt-dump-oops\n", + "/usr/bin/abrt-dump-xorg\n", + 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"/usr/bin/cancel.cups\n", + "/usr/bin/captoinfo\n", + "/usr/bin/cat\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/usr/bin/catchsegv\n", + "/usr/bin/catman\n", + "/usr/bin/cc\n", + "/usr/bin/ccomps\n", + "/usr/bin/cd\n", + "/usr/bin/cd-create-profile\n", + "/usr/bin/cdda2ogg\n", + "/usr/bin/cdda2wav\n", + "/usr/bin/cdda-player\n", + "/usr/bin/cd-drive\n", + "/usr/bin/cd-fix-profile\n", + "/usr/bin/cd-iccdump\n", + "/usr/bin/cd-info\n", + "/usr/bin/cd-it8\n", + "/usr/bin/cdparanoia\n", + "/usr/bin/cd-paranoia\n", + "/usr/bin/cdrdao\n", + "/usr/bin/cd-read\n", + "/usr/bin/cdrecord\n", + "/usr/bin/celtdec051\n", + "/usr/bin/celtenc051\n", + "/usr/bin/centrino-decode\n", + "/usr/bin/certmaster-getcert\n", + "/usr/bin/certtool\n", + "/usr/bin/certutil\n", + "/usr/bin/cfadmin\n", + "/usr/bin/c++filt\n", + "/usr/bin/cgclassify\n", + "/usr/bin/cgcreate\n", + "/usr/bin/cgdelete\n", + "/usr/bin/cgexec\n", + "/usr/bin/cgget\n", + "/usr/bin/cgset\n", + 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"/usr/bin/debuginfo-install\n", + "/usr/bin/desktop-file-install\n", + "/usr/bin/desktop-file-validate\n", + "/usr/bin/detect_ppa\n", + "/usr/bin/dgawk\n", + "/usr/bin/diff-jars\n", + "/usr/bin/diffstat\n", + "/usr/bin/dijkstra\n", + "/usr/bin/dimax_init\n", + "/usr/bin/dircolors\n", + "/usr/bin/dirname\n", + "/usr/bin/dislocate\n", + "/usr/bin/display\n", + "/usr/bin/dnsdomainname\n", + "/usr/bin/domainname\n", + "/usr/bin/dotlockfile\n", + "/usr/bin/dracut\n", + "/usr/bin/dtestcm\n", + "/usr/bin/dtrace\n", + "/usr/bin/dvcont\n", + "/usr/bin/dvd-ram-control\n", + "/usr/bin/dvdrecord\n", + "/usr/bin/dvd+rw-format\n", + "/usr/bin/dvd+rw-mediainfo\n", + "/usr/bin/dvi2fax\n", + "/usr/bin/dvilualatex\n", + "/usr/bin/dviluatex\n", + "/usr/bin/dynamodb_dump\n", + "/usr/bin/dynamodb_load\n", + "/usr/bin/easy_install\n", + "/usr/bin/easy_install-2.7\n", + "/usr/bin/easy_install-3.6\n", + "/usr/bin/echo\n", + "/usr/bin/edid-decode\n", + "/usr/bin/eject\n", + "/usr/bin/elbadmin\n", + 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"/usr/bin/fallocate\n", + "/usr/bin/false\n", + "/usr/bin/fc\n", + "/usr/bin/fc-cache\n", + "/usr/bin/fc-cache-32\n", + "/usr/bin/fc-cache-64\n", + "/usr/bin/fc-cat\n", + "/usr/bin/fc-conflist\n", + "/usr/bin/fc-list\n", + "/usr/bin/fc-match\n", + "/usr/bin/fc-pattern\n", + "/usr/bin/fc-query\n", + "/usr/bin/fc-scan\n", + "/usr/bin/fc-validate\n", + "/usr/bin/festival\n", + "/usr/bin/festival_client\n", + "/usr/bin/festival_server\n", + "/usr/bin/festival_server_control\n", + "/usr/bin/fetch_file\n", + "/usr/bin/ffcfstress\n", + "/usr/bin/ffmvforce\n", + "/usr/bin/fgconsole\n", + "/usr/bin/filebeat\n", + "/usr/bin/filezilla\n", + "/usr/bin/find-jar\n", + "/usr/bin/find-repos-of-install\n", + "/usr/bin/fipscheck\n", + "/usr/bin/fipshmac\n", + "/usr/bin/firewall-cmd\n", + "/usr/bin/firewall-config\n", + "/usr/bin/firewall-offline-cmd\n", + "/usr/bin/fixcvsdiff\n", + "/usr/bin/fixqt4headers.pl\n", + "/usr/bin/flatpak\n", + "/usr/bin/flock\n", + "/usr/bin/foomatic-rip\n", + "/usr/bin/freetype-config\n", + "/usr/bin/ftp-rfc\n", + "/usr/bin/fwtrace\n", + "/usr/bin/gapplication\n", + "/usr/bin/gatttool\n", + "/usr/bin/gawk\n", + "/usr/bin/gc\n", + "/usr/bin/gcc\n", + "/usr/bin/gcc-ar\n", + "/usr/bin/gcc-nm\n", + "/usr/bin/gcc-ranlib\n", + "/usr/bin/gconf-merge-tree\n", + "/usr/bin/gconftool-2\n", + "/usr/bin/gcore\n", + "/usr/bin/gcov\n", + "/usr/bin/gcr-viewer\n", + "/usr/bin/gctags\n", + "/usr/bin/gdb-add-index\n", + "/usr/bin/gdk-pixbuf-query-loaders-64\n", + "/usr/bin/gdk-pixbuf-thumbnailer\n", + "/usr/bin/gdm-screenshot\n", + "/usr/bin/gencat\n", + "/usr/bin/genisoimage\n", + "/usr/bin/genl-ctrl-list\n", + "/usr/bin/geoipupdate\n", + "/usr/bin/getcert\n", + "/usr/bin/getcifsacl\n", + "/usr/bin/getconf\n", + "/usr/bin/getfacl\n", + "/usr/bin/getfattr\n", + "/usr/bin/getkeycodes\n", + "/usr/bin/gflags_completions.sh\n", + "/usr/bin/gfortran\n", + "/usr/bin/ghostscript\n", + "/usr/bin/git-receive-pack\n", + "/usr/bin/git-upload-archive\n", + "/usr/bin/git-upload-pack\n", + "/usr/bin/gjs-console\n", + "/usr/bin/gkbd-keyboard-display\n", + "/usr/bin/glacier\n", + "/usr/bin/glance\n", + "/usr/bin/glance-2\n", + "/usr/bin/glance-2.7\n", + "/usr/bin/glib-compile-schemas\n", + "/usr/bin/globaltime\n", + "/usr/bin/glxgears\n", + "/usr/bin/gmake\n", + "/usr/bin/gnome-abrt\n", + "/usr/bin/gnome-character-map\n", + "/usr/bin/gnome-control-center\n", + "/usr/bin/gnome-keyring-daemon\n", + "/usr/bin/gnome-session-custom-session\n", + "/usr/bin/gnome-session-selector\n", + "/usr/bin/gnome-terminal\n", + "/usr/bin/gnuplot-minimal\n", + "/usr/bin/gnutls-cli\n", + "/usr/bin/gnutls-cli-debug\n", + "/usr/bin/gparted\n", + "/usr/bin/gpasswd\n", + "/usr/bin/gpg-agent\n", + "/usr/bin/gpgconf\n", + "/usr/bin/gpg-connect-agent\n", + "/usr/bin/gpg-error-config\n", + "/usr/bin/gpgparsemail\n", + "/usr/bin/gpic\n", + "/usr/bin/graphml2gv\n", + "/usr/bin/grep-changelog\n", + "/usr/bin/grl-inspect-0.3\n", + "/usr/bin/grl-launch-0.3\n", + "/usr/bin/grub2-kbdcomp\n", + "/usr/bin/grub2-menulst2cfg\n", + "/usr/bin/grub2-mkimage\n", + "/usr/bin/grub2-mklayout\n", + "/usr/bin/grub2-mkpasswd-pbkdf2\n", + "/usr/bin/grub2-mkrelpath\n", + "/usr/bin/grub2-mkrescue\n", + "/usr/bin/grub2-mkstandalone\n", + "/usr/bin/grub2-render-label\n", + "/usr/bin/grub2-script-check\n", + "/usr/bin/grub2-syslinux2cfg\n", + "/usr/bin/gsettings-data-convert\n", + "/usr/bin/gsf-office-thumbnailer\n", + "/usr/bin/gss-client\n", + "/usr/bin/gstack\n", + "/usr/bin/gst-feedback\n", + "/usr/bin/gst-feedback-0.10\n", + "/usr/bin/gst-inspect\n", + "/usr/bin/gst-inspect-0.10\n", + "/usr/bin/gst-inspect-1.0\n", + "/usr/bin/gst-launch\n", + "/usr/bin/gst-launch-0.10\n", + "/usr/bin/gst-launch-1.0\n", + "/usr/bin/gst-stats-1.0\n", + "/usr/bin/gst-xmlinspect\n", + "/usr/bin/gst-xmlinspect-0.10\n", + "/usr/bin/gst-xmllaunch\n", + "/usr/bin/gst-xmllaunch-0.10\n", + "/usr/bin/gtar\n", + "/usr/bin/gtk-launch\n", + "/usr/bin/gtk-update-icon-cache\n", + "/usr/bin/gucharmap\n", + "/usr/bin/gunicorn\n", + "/usr/bin/gunicorn_paster\n", + "/usr/bin/gupnp-dlna-info-2.0\n", + "/usr/bin/gupnp-dlna-ls-profiles-2.0\n", + "/usr/bin/gvcolor\n", + "/usr/bin/gvfs-cat\n", + "/usr/bin/gvfs-copy\n", + "/usr/bin/gvfs-rename\n", + "/usr/bin/gvfs-save\n", + "/usr/bin/gvfs-set-attribute\n", + "/usr/bin/gvfs-trash\n", + "/usr/bin/gvmap\n", + "/usr/bin/gvmap.sh\n", + "/usr/bin/gvpack\n", + "/usr/bin/hangul\n", + "/usr/bin/hca_self_test.ofed\n", + "/usr/bin/hciattach\n", + "/usr/bin/hciconfig\n", + "/usr/bin/hcidump\n", + "/usr/bin/hcitool\n", + "/usr/bin/hdsploader\n", + "/usr/bin/head\n", + "/usr/bin/heat\n", + "/usr/bin/heat-2\n", + "/usr/bin/heat-2.7\n", + "/usr/bin/hex2hcd\n", + "/usr/bin/hmac256\n", + "/usr/bin/hostname\n", + "/usr/bin/hostnamectl\n", + "/usr/bin/hpcups-update-ppds\n", + "/usr/bin/htcontext\n", + "/usr/bin/htlatex\n", + "/usr/bin/htxelatex\n", + "/usr/bin/hwloc-annotate\n", + "/usr/bin/hwloc-assembler\n", + "/usr/bin/hwloc-assembler-remote\n", + "/usr/bin/hwloc-bind\n", + "/usr/bin/hwloc-calc\n", + "/usr/bin/hwloc-compress-dir\n", + "/usr/bin/hwloc-diff\n", + "/usr/bin/hwloc-distances\n", + "/usr/bin/hwloc-distrib\n", + "/usr/bin/hwloc-gather-topology\n", + "/usr/bin/hwloc-info\n", + "/usr/bin/hwloc-ls\n", + "/usr/bin/hwloc-patch\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/usr/bin/hwloc-ps\n", + "/usr/bin/i2c\n", + "/usr/bin/ib_acme\n", + "/usr/bin/ib_atomic_bw\n", + "/usr/bin/ib_atomic_lat\n", + "/usr/bin/ibcongest\n", + "/usr/bin/ibdiagm.sh\n", + "/usr/bin/ibdiagnet\n", + "/usr/bin/ibdiagnet_csv2xml.py\n", + "/usr/bin/ibdiagpath\n", + "/usr/bin/ibdmchk\n", + "/usr/bin/ibnlparse\n", + "/usr/bin/ib_read_bw\n", + "/usr/bin/ib_read_lat\n", + "/usr/bin/ib_send_lat\n", + "/usr/bin/ibus-daemon\n", + "/usr/bin/ibus-table-createdb\n", + "/usr/bin/ibv_asyncwatch\n", + "/usr/bin/ibv_cc_pingpong\n", + "/usr/bin/ibv_dcini\n", + "/usr/bin/ibv_dctgt\n", + "/usr/bin/ibv_devices\n", + "/usr/bin/ibv_polldcinfo\n", + "/usr/bin/ibv_rc_pingpong\n", + "/usr/bin/ibv_task_pingpong\n", + "/usr/bin/ibv_uc_pingpong\n", + "/usr/bin/ib_write_lat\n", + "/usr/bin/iceauth\n", + "/usr/bin/icedax\n", + "/usr/bin/iconv\n", + "/usr/bin/idiag-socket-details\n", + "/usr/bin/iecset\n", + "/usr/bin/ifnames\n", + "/usr/bin/igawk\n", + "/usr/bin/implantisomd5\n", + "/usr/bin/infocmp\n", + "/usr/bin/infotocap\n", + "/usr/bin/inputattach\n", + "/usr/bin/install\n", + "/usr/bin/install-printerdriver\n", + "/usr/bin/instance_events\n", + "/usr/bin/intltool-extract\n", + "/usr/bin/intltool-prepare\n", + "/usr/bin/intltool-update\n", + "/usr/bin/ionice\n", + "/usr/bin/iostat\n", + "/usr/bin/ipa-getcert\n", + "/usr/bin/ipcalc\n", + "/usr/bin/ipcmk\n", + "/usr/bin/ipcrm\n", + "/usr/bin/ipcs\n", + "/usr/bin/ipmicmd\n", + "/usr/bin/ipmilan\n", + "/usr/bin/ipod-read-sysinfo-extended\n", + "/usr/bin/iptables-xml\n", + "/usr/bin/iptc\n", + "/usr/bin/isdv4-serial-inputattach\n", + "/usr/bin/iso-read\n", + "/usr/bin/itrace\n", + "/usr/bin/jadetex\n", + "/usr/bin/java\n", + "/usr/bin/javaws\n", + "/usr/bin/javaws.itweb\n", + "/usr/bin/journalctl\n", + "/usr/bin/jscal\n", + "/usr/bin/jscal-restore\n", + "/usr/bin/jscal-store\n", + "/usr/bin/jsonpatch\n", + "/usr/bin/jsonpatch-2\n", + "/usr/bin/jsonpatch-2.7\n", + "/usr/bin/json_reformat\n", + "/usr/bin/jsonschema\n", + "/usr/bin/jvmjar\n", + "/usr/bin/kadmin\n", + "/usr/bin/kbdrate\n", + "/usr/bin/kdumpctl\n", + "/usr/bin/kernel-install\n", + "/usr/bin/keyctl\n", + "/usr/bin/killall\n", + "/usr/bin/kill_instance\n", + "/usr/bin/kpasswd\n", + "/usr/bin/kpseaccess\n", + "/usr/bin/kpsepath\n", + "/usr/bin/kpsereadlink\n", + "/usr/bin/kpsestat\n", + "/usr/bin/kpsewhich\n", + "/usr/bin/kpsexpand\n", + "/usr/bin/krb5-config\n", + "/usr/bin/ksflatten\n", + "/usr/bin/ksvalidator\n", + "/usr/bin/kswitch\n", + "/usr/bin/last\n", + "/usr/bin/lastb\n", + "/usr/bin/lastcomm\n", + "/usr/bin/lastlog\n", + "/usr/bin/latex\n", + "/usr/bin/launch_instance\n", + "/usr/bin/lchfn\n", + "/usr/bin/lchsh\n", + "/usr/bin/ldapadd\n", + "/usr/bin/ldapcompare\n", + "/usr/bin/ldapdelete\n", + "/usr/bin/ldapexop\n", + "/usr/bin/ldapmodify\n", + "/usr/bin/ldapmodrdn\n", + "/usr/bin/ldappasswd\n", + "/usr/bin/ldapsearch\n", + "/usr/bin/ldapurl\n", + "/usr/bin/ldapwhoami\n", + "/usr/bin/ldns-chaos\n", + "/usr/bin/ldns-compare-zones\n", + "/usr/bin/ldns-dane\n", + "/usr/bin/ldns-dpa\n", + "/usr/bin/ldns-keyfetcher\n", + "/usr/bin/ldns-nsec3-hash\n", + "/usr/bin/ldns-read-zone\n", + "/usr/bin/ldns-update\n", + "/usr/bin/ldns-walk\n", + "/usr/bin/ldns-zcat\n", + "/usr/bin/lessecho\n", + "/usr/bin/libbluray_test\n", + "/usr/bin/libgcrypt-config\n", + "/usr/bin/libinput-list-devices\n", + "/usr/bin/libnetcfg\n", + "/usr/bin/libpng15-config\n", + "/usr/bin/libpng-config\n", + "/usr/bin/libreoffice\n", + "/usr/bin/libtar\n", + "/usr/bin/libwacom-list-local-devices\n", + "/usr/bin/list_instances\n", + "/usr/bin/lneato\n", + "/usr/bin/loadkeys\n", + "/usr/bin/loadunimap\n", + "/usr/bin/locale\n", + "/usr/bin/localectl\n", + "/usr/bin/localedef\n", + "/usr/bin/local-getcert\n", + "/usr/bin/locate\n", + "/usr/bin/loginctl\n", + "/usr/bin/logname\n", + "/usr/bin/lp.cups\n", + "/usr/bin/lppasswd\n", + "/usr/bin/lpq.cups\n", + "/usr/bin/lpr.cups\n", + "/usr/bin/lprm.cups\n", + "/usr/bin/lpstat\n", + "/usr/bin/lpstat.cups\n", + "/usr/bin/lpunlock\n", + "/usr/bin/lsattr\n", + "/usr/bin/lsb_release\n", + "/usr/bin/lscgroup\n", + "/usr/bin/lscpu\n", + "/usr/bin/lsipc\n", + "/usr/bin/lslocks\n", + "/usr/bin/lsmcli\n", + "/usr/bin/lsscsi\n", + "/usr/bin/lstopo-no-graphics\n", + "/usr/bin/lua\n", + "/usr/bin/luac\n", + "/usr/bin/lualatex\n", + "/usr/bin/luatex\n", + "/usr/bin/lwp-download\n", + "/usr/bin/lz4c\n", + "/usr/bin/lz4cat\n", + "/usr/bin/m17n-conv\n", + "/usr/bin/mac2unix\n", + "/usr/bin/machinectl\n", + "/usr/bin/mail\n", + "/usr/bin/Mail\n", + "/usr/bin/mailq\n", + "/usr/bin/mailq.postfix\n", + "/usr/bin/mailx\n", + "/usr/bin/make\n", + "/usr/bin/makedb\n", + "/usr/bin/makedeltarpm\n", + "/usr/bin/makeglossaries\n", + "/usr/bin/makeindex\n", + "/usr/bin/makeinfo\n", + "/usr/bin/mako-render\n", + "/usr/bin/man\n", + "/usr/bin/mandb\n", + "/usr/bin/manpath\n", + "/usr/bin/mapscrn\n", + "/usr/bin/marco\n", + "/usr/bin/marco-message\n", + "/usr/bin/mate-about\n", + "/usr/bin/mate-about-me\n", + "/usr/bin/mate-appearance-properties\n", + "/usr/bin/mate-at-properties\n", + "/usr/bin/mate-calc\n", + "/usr/bin/mate-calc-cmd\n", + "/usr/bin/mate-calculator\n", + "/usr/bin/mate-color-select\n", + "/usr/bin/mate-control-center\n", + "/usr/bin/mate-cpufreq-selector\n", + "/usr/bin/mate-default-applications-properties\n", + "/usr/bin/mate-desktop-item-edit\n", + "/usr/bin/mate-dictionary\n", + "/usr/bin/mate-disk-usage-analyzer\n", + "/usr/bin/mate-display-properties\n", + "/usr/bin/mate-font-viewer\n", + "/usr/bin/mate-invest-chart\n", + "/usr/bin/mate-keybinding-properties\n", + "/usr/bin/mate-keyboard-properties\n", + "/usr/bin/mate-mouse-properties\n", + "/usr/bin/mate-network-properties\n", + "/usr/bin/mate-notification-properties\n", + "/usr/bin/mate-panel\n", + "/usr/bin/mate-panel-screenshot\n", + "/usr/bin/mate-panel-test-applets\n", + "/usr/bin/mate-power-manager\n", + "/usr/bin/mate-power-preferences\n", + "/usr/bin/mate-power-statistics\n", + "/usr/bin/mate-screensaver\n", + "/usr/bin/mate-screensaver-command\n", + "/usr/bin/mate-screensaver-preferences\n", + "/usr/bin/mate-screenshot\n", + "/usr/bin/mate-search-tool\n", + "/usr/bin/mate-session\n", + "/usr/bin/mate-session-inhibit\n", + "/usr/bin/mate-session-properties\n", + "/usr/bin/mate-session-save\n", + "/usr/bin/mate-system-log\n", + "/usr/bin/mate-system-monitor\n", + "/usr/bin/mate-terminal\n", + "/usr/bin/mate-terminal.wrapper\n", + "/usr/bin/mate-thumbnail-font\n", + "/usr/bin/mate-typing-monitor\n", + "/usr/bin/mate-volume-control\n", + "/usr/bin/mate-volume-control-applet\n", + "/usr/bin/mate-window-properties\n", + "/usr/bin/mate-wm\n", + "/usr/bin/mattrib\n", + "/usr/bin/mbadblocks\n", + "/usr/bin/mbimcli\n", + "/usr/bin/mcat\n", + "/usr/bin/mcd\n", + "/usr/bin/mcheck\n", + "/usr/bin/mckey\n", + "/usr/bin/mclasserase\n", + "/usr/bin/mcomp\n", + "/usr/bin/mcookie\n", + "/usr/bin/mcopy\n", + "/usr/bin/mcra\n", + "/usr/bin/mc-tool\n", + "/usr/bin/mc-wait-for-name\n", + "/usr/bin/mdevices_info\n", + "/usr/bin/metacity\n", + "/usr/bin/metacity-message\n", + "/usr/bin/metricbeat\n", + "/usr/bin/mformat\n", + "/usr/bin/mfplain\n", + "/usr/bin/mft_uninstall.sh\n", + "/usr/bin/mib2c\n", + "/usr/bin/mib2c-update\n", + "/usr/bin/migratepages\n", + "/usr/bin/minicom\n", + "/usr/bin/mixartloader\n", + "/usr/bin/mkafmmap\n", + "/usr/bin/mkfontscale\n", + "/usr/bin/mkluatexfontdb\n", + "/usr/bin/mkmanifest\n", + "/usr/bin/mkocp\n", + "/usr/bin/mkpasswd\n", + "/usr/bin/mkrfc2734\n", + "/usr/bin/mlabel\n", + "/usr/bin/mlnx_conf_mgr.sh\n", + "/usr/bin/mlnx_dump_parser\n", + "/usr/bin/mlnx_interface_mgr.sh\n", + "/usr/bin/mlnx_qcn\n", + "/usr/bin/mlxcables\n", + "/usr/bin/mlxcables_ext\n", + "/usr/bin/mlxconfig\n", + "/usr/bin/mlx_fpga\n", + "/usr/bin/mlx_fpga_ext\n", + "/usr/bin/mlxfwmanager\n", + "/usr/bin/mlxgearbox\n", + "/usr/bin/mlxi2c\n", + "/usr/bin/mlxmcg\n", + "/usr/bin/mlxpci\n", + "/usr/bin/mlxtrace\n", + "/usr/bin/mlxtrace_ext\n", + "/usr/bin/mmcli\n", + "/usr/bin/mmc-tool\n", + "/usr/bin/moc-qt5\n", + "/usr/bin/montage\n", + "/usr/bin/mousetweaks\n", + "/usr/bin/mpartition\n", + "/usr/bin/mpaste\n", + "/usr/bin/mpi-selector\n", + "/usr/bin/mpi-selector-menu\n", + "/usr/bin/mpstat\n", + "/usr/bin/msgattrib\n", + "/usr/bin/msgcat\n", + "/usr/bin/msgcmp\n", + "/usr/bin/msgcomm\n", + "/usr/bin/msgconv\n", + "/usr/bin/msgexec\n", + "/usr/bin/msghack\n", + "/usr/bin/mshortname\n", + "/usr/bin/mshowfat\n", + "/usr/bin/mstarchive\n", + "/usr/bin/mst_cable\n", + "/usr/bin/mstconfig\n", + "/usr/bin/mstcongestion\n", + "/usr/bin/mstfwmanager\n", + "/usr/bin/mstfwtrace\n", + "/usr/bin/mst_ib_add\n", + "/usr/bin/mstmcra\n", + "/usr/bin/mstmread\n", + "/usr/bin/mstresourcedump\n", + "/usr/bin/mvxattr\n", + "/usr/bin/mx-create-image-cache\n", + "/usr/bin/mxtar\n", + "/usr/bin/mysql_config\n", + "/usr/bin/nail\n", + "/usr/bin/named-rrchecker\n", + "/usr/bin/namei\n", + "/usr/bin/nano\n", + "/usr/bin/natpmpc\n", + "/usr/bin/nautilus\n", + "/usr/bin/nautilus-autorun-software\n", + "/usr/bin/nautilus-desktop\n", + "/usr/bin/nautilus-sendto\n", + "/usr/bin/nc\n", + "/usr/bin/ncat\n", + "/usr/bin/ncurses5-config\n", + "/usr/bin/ncursesw5-config\n", + "/usr/bin/ndctl\n", + "/usr/bin/neato\n", + "/usr/bin/needs-restarting\n", + "/usr/bin/nenscript\n", + "/usr/bin/netaddr\n", + "/usr/bin/net-snmp-cert\n", + "/usr/bin/net-snmp-config\n", + "/usr/bin/net-snmp-config-x86_64\n", + "/usr/bin/net-snmp-create-v3-user\n", + "/usr/bin/netstat\n", + "/usr/bin/nettle-hash\n", + "/usr/bin/nettle-lfib-stream\n", + "/usr/bin/newaliases\n", + "/usr/bin/newaliases.postfix\n", + "/usr/bin/newgidmap\n", + "/usr/bin/newuidmap\n", + "/usr/bin/nf-ct-add\n", + "/usr/bin/nf-ct-list\n", + "/usr/bin/nf-exp-add\n", + "/usr/bin/nfs4_editfacl\n", + "/usr/bin/nfs4_getfacl\n", + "/usr/bin/nfs4_setfacl\n", + "/usr/bin/nfsiostat-sysstat\n", + "/usr/bin/nice\n", + "/usr/bin/nisdomainname\n", + "/usr/bin/nl-addr-add\n", + "/usr/bin/nl-addr-delete\n", + "/usr/bin/nl-addr-list\n", + "/usr/bin/nl-class-add\n", + "/usr/bin/nl-class-delete\n", + "/usr/bin/nl-classid-lookup\n", + "/usr/bin/nl-class-list\n", + "/usr/bin/nl-cls-add\n", + "/usr/bin/nl-cls-delete\n", + "/usr/bin/nl-cls-list\n", + "/usr/bin/nl-link-enslave\n", + "/usr/bin/nl-link-ifindex2name\n", + "/usr/bin/nl-link-name2ifindex\n", + "/usr/bin/nl-link-release\n", + "/usr/bin/nl-link-stats\n", + "/usr/bin/nl-list-caches\n", + "/usr/bin/nl-list-sockets\n", + "/usr/bin/nl-neigh-add\n", + "/usr/bin/nl-pktloc-lookup\n", + "/usr/bin/nl-qdisc-add\n", + "/usr/bin/nl-qdisc-delete\n", + "/usr/bin/nl-qdisc-list\n", + "/usr/bin/nl-route-add\n", + "/usr/bin/nl-tctree-list\n", + "/usr/bin/nl-util-addr\n", + "/usr/bin/nm-applet\n", + "/usr/bin/nmcli\n", + "/usr/bin/nm-connection-editor\n", + "/usr/bin/nmtui-connect\n", + "/usr/bin/nmtui-hostname\n", + "/usr/bin/nova\n", + "/usr/bin/nova-2\n", + "/usr/bin/nova-2.7\n", + "/usr/bin/nproc\n", + "/usr/bin/nss-policy-check\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/usr/bin/nsupdate\n", + "/usr/bin/ntpstat\n", + "/usr/bin/numactl\n", + "/usr/bin/numad\n", + "/usr/bin/numademo\n", + "/usr/bin/numastat\n", + "/usr/bin/nxagent\n", + "/usr/bin/objcopy\n", + "/usr/bin/ocs\n", + "/usr/bin/ocsptool\n", + "/usr/bin/odbc_config\n", + "/usr/bin/odbcinst\n", + "/usr/bin/oggdec\n", + "/usr/bin/oggenc\n", + "/usr/bin/oLschema2ldif\n", + "/usr/bin/on_ac_power\n", + "/usr/bin/oocalc\n", + "/usr/bin/oodraw\n", + "/usr/bin/ooffice\n", + "/usr/bin/ooviewdoc\n", + "/usr/bin/openipmicmd\n", + "/usr/bin/openoffice.org\n", + "/usr/bin/openstack-inventory\n", + "/usr/bin/orage\n", + "/usr/bin/orca\n", + "/usr/bin/orc-bugreport\n", + "/usr/bin/osage\n", + "/usr/bin/osinfo-db-path\n", + "/usr/bin/osinfo-db-validate\n", + "/usr/bin/osinfo-detect\n", + "/usr/bin/osinfo-install-script\n", + "/usr/bin/oslo-config-generator\n", + "/usr/bin/pacat\n", + "/usr/bin/pack200\n", + "/usr/bin/package-cleanup\n", + "/usr/bin/package-stash-conflicts\n", + "/usr/bin/pacmd\n", + "/usr/bin/pactl\n", + "/usr/bin/padsp\n", + "/usr/bin/padsp-32\n", + "/usr/bin/page\n", + "/usr/bin/pamon\n", + "/usr/bin/pam-panel-icon\n", + "/usr/bin/panelctl\n", + "/usr/bin/pango-list\n", + "/usr/bin/pango-querymodules-64\n", + "/usr/bin/pango-view\n", + "/usr/bin/paperconf\n", + "/usr/bin/papi_avail\n", + "/usr/bin/papi_clockres\n", + "/usr/bin/papi_command_line\n", + "/usr/bin/papi_component_avail\n", + "/usr/bin/papi_cost\n", + "/usr/bin/papi_decode\n", + "/usr/bin/papi_error_codes\n", + "/usr/bin/papi_event_chooser\n", + "/usr/bin/papi_mem_info\n", + "/usr/bin/papi_multiplex_cost\n", + "/usr/bin/papi_native_avail\n", + "/usr/bin/papi_version\n", + "/usr/bin/papi_xml_event_info\n", + "/usr/bin/paplay\n", + "/usr/bin/paps\n", + "/usr/bin/parec\n", + "/usr/bin/parecord\n", + "/usr/bin/passenger\n", + "/usr/bin/passenger-config\n", + "/usr/bin/passmass\n", + "/usr/bin/passwd\n", + "/usr/bin/paste\n", + "/usr/bin/pasuspender\n", + "/usr/bin/patch\n", + "/usr/bin/patchwork\n", + "/usr/bin/pathchk\n", + "/usr/bin/pavucontrol\n", + "/usr/bin/pax\n", + "/usr/bin/pax11publish\n", + "/usr/bin/pbm2ppa\n", + "/usr/bin/pchrt\n", + "/usr/bin/pckt_drop\n", + "/usr/bin/pcre-config\n", + "/usr/bin/pdf2dsc\n", + "/usr/bin/pdfdetach\n", + "/usr/bin/pdfimages\n", + "/usr/bin/pdfjadetex\n", + "/usr/bin/pdflatex\n", + "/usr/bin/pdfseparate\n", + "/usr/bin/pdftocairo\n", + "/usr/bin/perldoc\n", + "/usr/bin/perlthanks\n", + "/usr/bin/pf2afm\n", + "/usr/bin/pfbtopfa\n", + "/usr/bin/pfc\n", + "/usr/bin/pflags\n", + "/usr/bin/pgawk\n", + "/usr/bin/pic\n", + "/usr/bin/piconv\n", + "/usr/bin/pidstat\n", + "/usr/bin/pinentry-curses\n", + "/usr/bin/pitchplay\n", + "/usr/bin/pkaction\n", + "/usr/bin/pkcheck\n", + "/usr/bin/pkcs1-conv\n", + "/usr/bin/pkexec\n", + "/usr/bin/pkg-config\n", + "/usr/bin/pkla-admin-identities\n", + "/usr/bin/pkla-check-authorization\n", + "/usr/bin/pkttyagent\n", + "/usr/bin/play\n", + "/usr/bin/pluma\n", + "/usr/bin/pmap\n", + "/usr/bin/pnm2ppa\n", + "/usr/bin/pod2latex\n", + "/usr/bin/pod2man\n", + "/usr/bin/pod2usage\n", + "/usr/bin/podchecker\n", + "/usr/bin/podselect\n", + "/usr/bin/policyeditor\n", + "/usr/bin/policyeditor.itweb\n", + "/usr/bin/policytool\n", + "/usr/bin/powernow-k8-decode\n", + "/usr/bin/ppdc\n", + "/usr/bin/preconv\n", + "/usr/bin/printafm\n", + "/usr/bin/prtstat\n", + "/usr/bin/ps2ascii\n", + "/usr/bin/psfaddtable\n", + "/usr/bin/psfgettable\n", + "/usr/bin/psfstriptable\n", + "/usr/bin/psfxtable\n", + "/usr/bin/pstack\n", + "/usr/bin/pstruct\n", + "/usr/bin/ptaskset\n", + "/usr/bin/pulseaudio\n", + "/usr/bin/purple-client-example\n", + "/usr/bin/purple-send-async\n", + "/usr/bin/purple-url-handler\n", + "/usr/bin/pwhich\n", + "/usr/bin/pwmake\n", + "/usr/bin/pwscore\n", + "/usr/bin/pyami_sendmail\n", + "/usr/bin/pydoc\n", + "/usr/bin/pydoc3\n", + "/usr/bin/pydoc3.6\n", + "/usr/bin/pyrsa-decrypt\n", + "/usr/bin/pyrsa-decrypt-2\n", + "/usr/bin/pyrsa-decrypt-bigfile\n", + "/usr/bin/pyrsa-decrypt-bigfile-2\n", + "/usr/bin/pyrsa-encrypt\n", + "/usr/bin/pyrsa-encrypt-2\n", + "/usr/bin/pyrsa-encrypt-bigfile\n", + "/usr/bin/pyrsa-encrypt-bigfile-2\n", + "/usr/bin/pyrsa-keygen\n", + "/usr/bin/pyrsa-keygen-2\n", + "/usr/bin/pyrsa-priv2pub\n", + "/usr/bin/pyrsa-priv2pub-2\n", + "/usr/bin/pyrsa-sign\n", + "/usr/bin/pyrsa-sign-2\n", + "/usr/bin/pyrsa-verify\n", + "/usr/bin/pyrsa-verify-2\n", + "/usr/bin/python2.7-config\n", + "/usr/bin/python2-config\n", + "/usr/bin/python-config\n", + "/usr/bin/qdbuscpp2xml-qt5\n", + "/usr/bin/qdbusxml2cpp-qt5\n", + "/usr/bin/qemu-ga\n", + "/usr/bin/qlalr\n", + "/usr/bin/qmake-qt5\n", + "/usr/bin/qmicli\n", + "/usr/bin/quota\n", + "/usr/bin/quotasync\n", + "/usr/bin/rackup\n", + "/usr/bin/rake\n", + "/usr/bin/ranlib\n", + "/usr/bin/rapper\n", + "/usr/bin/rarian-example\n", + "/usr/bin/rarian-sk-config\n", + "/usr/bin/rarian-sk-extract\n", + "/usr/bin/rarian-sk-gen-uuid\n", + "/usr/bin/rarian-sk-get-cl\n", + "/usr/bin/rarian-sk-get-content-list\n", + "/usr/bin/rarian-sk-get-extended-content-list\n", + "/usr/bin/rarian-sk-get-scripts\n", + "/usr/bin/rarian-sk-install\n", + "/usr/bin/rarian-sk-migrate\n", + "/usr/bin/rarian-sk-preinstall\n", + "/usr/bin/rarian-sk-rebuild\n", + "/usr/bin/rarian-sk-update\n", + "/usr/bin/raw\n", + "/usr/bin/raw_ethernet_burst_lat\n", + "/usr/bin/raw_ethernet_bw\n", + "/usr/bin/raw_ethernet_fs_rate\n", + "/usr/bin/raw_ethernet_lat\n", + "/usr/bin/rcc-qt5\n", + "/usr/bin/rcopy\n", + "/usr/bin/rcs\n", + "/usr/bin/rcsclean\n", + "/usr/bin/rcsdiff\n", + "/usr/bin/rcsfreeze\n", + "/usr/bin/rcsmerge\n", + "/usr/bin/rct\n", + "/usr/bin/rctest\n", + "/usr/bin/rdate\n", + "/usr/bin/rdfproc\n", + "/usr/bin/rdma_client\n", + "/usr/bin/rdma_server\n", + "/usr/bin/rdma_xclient\n", + "/usr/bin/rdma_xserver\n", + "/usr/bin/rdoc\n", + "/usr/bin/read\n", + "/usr/bin/readcd\n", + "/usr/bin/readelf\n", + "/usr/bin/readlink\n", + "/usr/bin/readmult\n", + "/usr/bin/readom\n", + "/usr/bin/realpath\n", + "/usr/bin/rebuild-jar-repository\n", + "/usr/bin/rec\n", + "/usr/bin/recode\n", + "/usr/bin/recode-sr-latin\n", + "/usr/bin/recountdiff\n", + "/usr/bin/redhat_lsb_init\n", + "/usr/bin/redhat-support-tool\n", + "/usr/bin/redland-db-upgrade\n", + "/usr/bin/regpatch\n", + "/usr/bin/rename\n", + "/usr/bin/renice\n", + "/usr/bin/repoclosure\n", + "/usr/bin/repo-graph\n", + "/usr/bin/repomanage\n", + "/usr/bin/report-cli\n", + "/usr/bin/reporter-bugzilla\n", + "/usr/bin/reporter-mailx\n", + "/usr/bin/reporter-upload\n", + "/usr/bin/reposync\n", + "/usr/bin/repotrack\n", + "/usr/bin/rescan-scsi-bus.sh\n", + "/usr/bin/resizecons\n", + "/usr/bin/resourcedump\n", + "/usr/bin/rfcomm\n", + "/usr/bin/rhsmcertd\n", + "/usr/bin/rhythmbox-client\n", + "/usr/bin/riostream\n", + "/usr/bin/rlogin-cwd\n", + "/usr/bin/rmail\n", + "/usr/bin/rmail.postfix\n", + "/usr/bin/rmcp_ping\n", + "/usr/bin/rnano\n", + "/usr/bin/rpcclient\n", + "/usr/bin/rpcgen\n", + "/usr/bin/rpm2cpio\n", + "/usr/bin/rpmdumpheader\n", + "/usr/bin/rpmgraph\n", + "/usr/bin/rpmspec\n", + "/usr/bin/rstream\n", + "/usr/bin/rsync\n", + "/usr/bin/rsyslog-recover-qi.pl\n", + "/usr/bin/rumakeindex\n", + "/usr/bin/runcon\n", + "/usr/bin/run-parts\n", + "/usr/bin/run_perftest_loopback\n", + "/usr/bin/run_perftest_multi_devices\n", + "/usr/bin/runscript\n", + "/usr/bin/rxe_cfg\n", + "/usr/bin/sadf\n", + "/usr/bin/samba-regedit\n", + "/usr/bin/sandbox\n", + "/usr/bin/sane-find-scanner\n", + "/usr/bin/sar\n", + "/usr/bin/sas_disk_blink\n", + "/usr/bin/satyr\n", + "/usr/bin/saytime\n", + "/usr/bin/sbcdec\n", + "/usr/bin/sbcenc\n", + "/usr/bin/sbcinfo\n", + "/usr/bin/scanimage\n", + "/usr/bin/sccmap\n", + "/usr/bin/scl\n", + "/usr/bin/scl_enabled\n", + "/usr/bin/scl_source\n", + "/usr/bin/scmp_sys_resolver\n", + "/usr/bin/scp\n", + "/usr/bin/scp-dbus-service\n", + "/usr/bin/screen\n", + "/usr/bin/script\n", + "/usr/bin/scriptreplay\n", + "/usr/bin/scrollkeeper-config\n", + "/usr/bin/scrollkeeper-extract\n", + "/usr/bin/scrollkeeper-gen-seriesid\n", + "/usr/bin/scrollkeeper-get-cl\n", + "/usr/bin/scrollkeeper-get-content-list\n", + "/usr/bin/scrollkeeper-get-extended-content-list\n", + "/usr/bin/scrollkeeper-get-index-from-docpath\n", + "/usr/bin/scrollkeeper-get-toc-from-docpath\n", + "/usr/bin/scrollkeeper-get-toc-from-id\n", + "/usr/bin/scrollkeeper-install\n", + "/usr/bin/scrollkeeper-preinstall\n", + "/usr/bin/scrollkeeper-rebuilddb\n", + "/usr/bin/scrollkeeper-uninstall\n", + "/usr/bin/scrollkeeper-update\n", + "/usr/bin/scsi_ch_swp\n", + "/usr/bin/scsi_logging_level\n", + "/usr/bin/scsi_mandat\n", + "/usr/bin/scsi_readcap\n", + "/usr/bin/scsi_ready\n", + "/usr/bin/scsi-rescan\n", + "/usr/bin/scsi_satl\n", + "/usr/bin/scsi_start\n", + "/usr/bin/scsi_stop\n", + "/usr/bin/scsi_temperature\n", + "/usr/bin/sctp_darn\n", + "/usr/bin/sctp_status\n", + "/usr/bin/sctp_test\n", + "/usr/bin/sdbadmin\n", + "/usr/bin/sdparm\n", + "/usr/bin/sdp_long_message\n", + "/usr/bin/sdrcomp\n", + "/usr/bin/seahorse\n", + "/usr/bin/sealert\n", + "/usr/bin/seapplet\n", + "/usr/bin/secon\n", + "/usr/bin/secret-tool\n", + "/usr/bin/selfsign-getcert\n", + "/usr/bin/semodule_package\n", + "/usr/bin/setarch\n", + "/usr/bin/setcifsacl\n", + "/usr/bin/setfacl\n", + "/usr/bin/setfattr\n", + "/usr/bin/setkeycodes\n", + "/usr/bin/setmetamode\n", + "/usr/bin/setserial\n", + "/usr/bin/setxkbmap\n", + "/usr/bin/sexp-conv\n", + "/usr/bin/sfconv\n", + "/usr/bin/sg_compare_and_write\n", + "/usr/bin/sg_copy_results\n", + "/usr/bin/sg_decode_sense\n", + "/usr/bin/sg_emc_trespass\n", + "/usr/bin/sg_format\n", + "/usr/bin/sg_get_config\n", + "/usr/bin/sg_get_lba_status\n", + "/usr/bin/sg_map\n", + "/usr/bin/sg_map26\n", + "/usr/bin/sg_opcodes\n", + "/usr/bin/sg_raw\n", + "/usr/bin/sg_rdac\n", + "/usr/bin/sg_read\n", + "/usr/bin/sg_read_block_limits\n", + "/usr/bin/sg_read_buffer\n", + "/usr/bin/sg_readcap\n", + "/usr/bin/sg_read_long\n", + "/usr/bin/sg_reassign\n", + "/usr/bin/sg_referrals\n", + "/usr/bin/sg_safte\n", + "/usr/bin/sg_sanitize\n", + "/usr/bin/sg_sat_identify\n", + "/usr/bin/sg_sat_phy_event\n", + "/usr/bin/sg_sat_set_features\n", + "/usr/bin/sg_scan\n", + "/usr/bin/sg_senddiag\n", + "/usr/bin/sg_start\n", + "/usr/bin/sg_sync\n", + "/usr/bin/sg_unmap\n", + "/usr/bin/sg_write_same\n", + "/usr/bin/sg_xcopy\n", + "/usr/bin/sha1sum\n", + "/usr/bin/sha224sum\n", + "/usr/bin/sha256sum\n", + "/usr/bin/sha384sum\n", + "/usr/bin/sha512sum\n", + "/usr/bin/sharesec\n", + "/usr/bin/shasum\n", + "/usr/bin/shcomp\n", + "/usr/bin/show-changed-rco\n", + "/usr/bin/showconsolefont\n", + "/usr/bin/show-installed\n", + "/usr/bin/sim_client\n", + "/usr/bin/simc_lsmplugin\n", + "/usr/bin/simple-scan\n", + "/usr/bin/slabtop\n", + "/usr/bin/sliceprint\n", + "/usr/bin/smbcacls\n", + "/usr/bin/smbclient\n", + "/usr/bin/smbcontrol\n", + "/usr/bin/smbcquotas\n", + "/usr/bin/smbpasswd\n", + "/usr/bin/smbtar\n", + "/usr/bin/sndfile-resample\n", + "/usr/bin/snice\n", + "/usr/bin/snmpconf\n", + "/usr/bin/soffice\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/usr/bin/soundstretch\n", + "/usr/bin/spax\n", + "/usr/bin/spd-conf\n", + "/usr/bin/spd-say\n", + "/usr/bin/speaker-test\n", + "/usr/bin/speech-dispatcher\n", + "/usr/bin/spice-vdagent\n", + "/usr/bin/splain\n", + "/usr/bin/ssh-add\n", + "/usr/bin/ssh-agent\n", + "/usr/bin/ssh-copy-id\n", + "/usr/bin/ssh-keyscan\n", + "/usr/bin/sshpass\n", + "/usr/bin/ssltap\n", + "/usr/bin/sss_ssh_authorizedkeys\n", + "/usr/bin/stap\n", + "/usr/bin/stapbpf\n", + "/usr/bin/stapdyn\n", + "/usr/bin/stap-merge\n", + "/usr/bin/stap-prep\n", + "/usr/bin/stap-report\n", + "/usr/bin/staprun\n", + "/usr/bin/stapsh\n", + "/usr/bin/start-pulseaudio-x11\n", + "/usr/bin/startx\n", + "/usr/bin/startxfce4\n", + "/usr/bin/stat\n", + "/usr/bin/states\n", + "/usr/bin/strace\n", + "/usr/bin/strace-log-merge\n", + "/usr/bin/stream\n", + "/usr/bin/stunbdc\n", + "/usr/bin/subscription-manager\n", + "/usr/bin/sudoreplay\n", + "/usr/bin/svnadmin\n", + "/usr/bin/svnsync\n", + "/usr/bin/sync\n", + "/usr/bin/synclient\n", + "/usr/bin/syncqt.pl\n", + "/usr/bin/syndaemon\n", + "/usr/bin/system-config-abrt\n", + "/usr/bin/system-config-date\n", + "/usr/bin/system-config-language\n", + "/usr/bin/system-config-printer\n", + "/usr/bin/system-config-printer-applet\n", + "/usr/bin/system-config-users\n", + "/usr/bin/systemctl\n", + "/usr/bin/systemd-analyze\n", + "/usr/bin/systemd-ask-password\n", + "/usr/bin/systemd-cat\n", + "/usr/bin/systemd-cgls\n", + "/usr/bin/systemd-cgtop\n", + "/usr/bin/systemd-coredumpctl\n", + "/usr/bin/systemd-delta\n", + "/usr/bin/systemd-detect-virt\n", + "/usr/bin/systemd-escape\n", + "/usr/bin/systemd-loginctl\n", + "/usr/bin/systemd-machine-id-setup\n", + "/usr/bin/systemd-nspawn\n", + "/usr/bin/systemd-path\n", + "/usr/bin/systemd-sysv-convert\n", + "/usr/bin/systemd-tty-ask-password-agent\n", + "/usr/bin/tabs\n", + "/usr/bin/tac\n", + "/usr/bin/tail\n", + "/usr/bin/tailf\n", + "/usr/bin/tapestat\n", + "/usr/bin/tar\n", + "/usr/bin/targetcli\n", + "/usr/bin/targetclid\n", + "/usr/bin/targetctl\n", + "/usr/bin/taskadmin\n", + "/usr/bin/taskset\n", + "/usr/bin/tcldocstrip\n", + "/usr/bin/tclsh\n", + "/usr/bin/tclsh8.5\n", + "/usr/bin/tcptraceroute\n", + "/usr/bin/tcsh\n", + "/usr/bin/tc_wrap.py\n", + "/usr/bin/teamd\n", + "/usr/bin/teamdctl\n", + "/usr/bin/teamnl\n", + "/usr/bin/teckit_compile\n", + "/usr/bin/telepathy-gabble-xmpp-console\n", + "/usr/bin/testlibraw\n", + "/usr/bin/testparm\n", + "/usr/bin/test_ppa\n", + "/usr/bin/texconfig\n", + "/usr/bin/texconfig-dialog\n", + "/usr/bin/texconfig-sys\n", + "/usr/bin/texhash\n", + "/usr/bin/texi2any\n", + "/usr/bin/texlua\n", + "/usr/bin/texluac\n", + "/usr/bin/text2wave\n", + "/usr/bin/thunar\n", + "/usr/bin/Thunar\n", + "/usr/bin/thunar-settings\n", + "/usr/bin/thunar-volman\n", + "/usr/bin/thunar-volman-settings\n", + "/usr/bin/tic\n", + "/usr/bin/timedatectl\n", + "/usr/bin/timed-read\n", + "/usr/bin/tload\n", + "/usr/bin/tnameserv\n", + "/usr/bin/toc2cddb\n", + "/usr/bin/toc2cue\n", + "/usr/bin/totem-video-thumbnailer\n", + "/usr/bin/touch\n", + "/usr/bin/tracepath\n", + "/usr/bin/tracepath6\n", + "/usr/bin/traceroute\n", + "/usr/bin/traceroute6\n", + "/usr/bin/tracker\n", + "/usr/bin/transmission-create\n", + "/usr/bin/transmission-edit\n", + "/usr/bin/transmission-gtk\n", + "/usr/bin/transmission-remote\n", + "/usr/bin/transmission-show\n", + "/usr/bin/traptoemail\n", + "/usr/bin/truncate\n", + "/usr/bin/turbostat\n", + "/usr/bin/txtconv\n", + "/usr/bin/tz_convert\n", + "/usr/bin/tzselect\n", + "/usr/bin/ucmatose\n", + "/usr/bin/ucs2any\n", + "/usr/bin/ucx_info\n", + "/usr/bin/ucx_perftest\n", + "/usr/bin/ucx_read_profile\n", + "/usr/bin/udaddy\n", + "/usr/bin/udevadm\n", + "/usr/bin/udisksctl\n", + "/usr/bin/uic-qt5\n", + "/usr/bin/ulockmgr_server\n", + "/usr/bin/umask\n", + "/usr/bin/unalias\n", + "/usr/bin/uname\n", + "/usr/bin/uncompress\n", + "/usr/bin/unexpand\n", + "/usr/bin/unflatten\n", + "/usr/bin/unicode_start\n", + "/usr/bin/unicode_stop\n", + "/usr/bin/unix2mac\n", + "/usr/bin/unoconv\n", + "/usr/bin/unpack200\n", + "/usr/bin/unshare\n", + "/usr/bin/unwrapdiff\n", + "/usr/bin/update-ca-trust\n", + "/usr/bin/updatedb\n", + "/usr/bin/update-desktop-database\n", + "/usr/bin/update-gtk-immodules\n", + "/usr/bin/update-mime-database\n", + "/usr/bin/updmap\n", + "/usr/bin/updmap-sys\n", + "/usr/bin/urlgrabber\n", + "/usr/bin/usb-devices\n", + "/usr/bin/userformat\n", + "/usr/bin/userpasswd\n", + "/usr/bin/usx2yloader\n", + "/usr/bin/uuclient\n", + "/usr/bin/vcut\n", + "/usr/bin/verify_blkparse\n", + "/usr/bin/VGAuthService\n", + "/usr/bin/vinagre\n", + "/usr/bin/virt-host-validate\n", + "/usr/bin/virt-pki-validate\n", + "/usr/bin/virt-xml-validate\n", + "/usr/bin/vlock\n", + "/usr/bin/vmmouse_detect\n", + "/usr/bin/vmstat\n", + "/usr/bin/vmware-checkvm\n", + "/usr/bin/vmware-hgfsclient\n", + "/usr/bin/vmware-namespace-cmd\n", + "/usr/bin/vmware-rpctool\n", + "/usr/bin/vmware-toolbox-cmd\n", + "/usr/bin/vmware-user\n", + "/usr/bin/vmware-user-suid-wrapper\n", + "/usr/bin/vmware-vgauth-cmd\n", + "/usr/bin/vmware-vmblock-fuse\n", + "/usr/bin/vmware-xferlogs\n", + "/usr/bin/vorbiscomment\n", + "/usr/bin/vpi_tcpdump\n", + "/usr/bin/vxloader\n", + "/usr/bin/wait\n", + "/usr/bin/waitmax\n", + "/usr/bin/wall\n", + "/usr/bin/watch\n", + "/usr/bin/watchgnupg\n", + "/usr/bin/wavpack\n", + "/usr/bin/wc\n", + "/usr/bin/wdctl\n", + "/usr/bin/weather\n", + "/usr/bin/websockify\n", + "/usr/bin/whatis\n", + "/usr/bin/which\n", + "/usr/bin/whiptail\n", + "/usr/bin/whoami\n", + "/usr/bin/withsctp\n", + "/usr/bin/wnck-urgency-monitor\n", + "/usr/bin/wvdial\n", + "/usr/bin/wvdialconf\n", + "/usr/bin/wvgain\n", + "/usr/bin/wvunpack\n", + "/usr/bin/x86_64-redhat-linux-c++\n", + "/usr/bin/x86_64-redhat-linux-g++\n", + "/usr/bin/x86_64-redhat-linux-gcc\n", + "/usr/bin/x86_energy_perf_policy\n", + "/usr/bin/xargs\n", + "/usr/bin/xauth\n", + "/usr/bin/xbrlapi\n", + "/usr/bin/xchat\n", + "/usr/bin/xdg-desktop-icon\n", + "/usr/bin/xdg-email\n", + "/usr/bin/xdg-icon-resource\n", + "/usr/bin/xdg-screensaver\n", + "/usr/bin/xdg-user-dirs-gtk-update\n", + "/usr/bin/xdg-user-dirs-update\n", + "/usr/bin/xdvi-xaw\n", + "/usr/bin/xelatex\n", + "/usr/bin/xfce4-accessibility-settings\n", + "/usr/bin/xfce4-appearance-settings\n", + "/usr/bin/xfce4-appfinder\n", + "/usr/bin/xfce4-display-settings\n", + "/usr/bin/xfce4-keyboard-settings\n", + "/usr/bin/xfce4-mime-settings\n", + "/usr/bin/xfce4-mouse-settings\n", + "/usr/bin/xfce4-panel\n", + "/usr/bin/xfce4-popup-applicationsmenu\n", + "/usr/bin/xfce4-popup-directorymenu\n", + "/usr/bin/xfce4-popup-windowmenu\n", + "/usr/bin/xfce4-power-manager\n", + "/usr/bin/xfce4-power-manager-settings\n", + "/usr/bin/xfce4-session\n", + "/usr/bin/xfce4-session-logout\n", + "/usr/bin/xfce4-session-settings\n", + "/usr/bin/xfce4-settings-editor\n", + "/usr/bin/xfce4-settings-manager\n", + "/usr/bin/xfce4-terminal\n", + "/usr/bin/xfconf-query\n", + "/usr/bin/xflock4\n", + "/usr/bin/xfwm4-tweaks-settings\n", + "/usr/bin/xfwm4-workspace-settings\n", + "/usr/bin/xgamma\n", + "/usr/bin/xkbcomp\n", + "/usr/bin/xlsatoms\n", + "/usr/bin/xlsclients\n", + "/usr/bin/xminicom\n", + "/usr/bin/xml2-config\n", + "/usr/bin/xmlcatalog\n", + "/usr/bin/xmlsec1\n", + "/usr/bin/xmodmap\n", + "/usr/bin/xorg-x11-fonts-update-dirs\n", + "/usr/bin/xrandr\n", + "/usr/bin/xsetwacom\n", + "/usr/bin/xslt-config\n", + "/usr/bin/xsltproc\n", + "/usr/bin/xstdcmap\n", + "/usr/bin/xvattr\n", + "/usr/bin/xzcat\n", + "/usr/bin/xzcmp\n", + "/usr/bin/xzdec\n", + "/usr/bin/yacc\n", + "/usr/bin/ypdomainname\n", + "/usr/bin/yum-config-manager\n", + "/usr/bin/yumdownloader\n", + "/usr/bin/yum-groups-manager\n", + "/usr/bin/zcat\n", + "/usr/bin/zcmp\n", + "/usr/bin/zforce\n", + "/usr/bin/zipcloak\n", + "/usr/bin/zipdetails\n" + ] + } + ], + "source": [ + "ls /usr/bin/c*\n", + "ls /usr/bin/*a*\n", + "ls /usr/bin/*o\n", + "ls /usr/bin/*[ac]*" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## History\n", + "\n", + "1. Checking the output of the history command, how many commands have you typed in so far?\n", + "2. Use the up arrow key to check the command you used before history command. What is it? Does it make sense?\n", + "3. Type several random characters on the command prompt. Can you bring the cursor to the start with Ctrl + A? Next, can you bring the cursor to the end with Ctrl + E? Finally, what happens when you use Ctrl + C?\n" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " 1 cd /data/project/leallab\n", + " 2 ls /ls\n", + " 3 ls -ls\n", + " 4 cd ics1515_genexus\n", + " 5 groups trinleb\n", + " 6 cd ics1515_genexus\n", + " 7 ls -ls\n", + " 8 cd ..\n", + " 9 ls -ls\n", + " 10 module avial\n", + " 11 pwd\n", + " 12 cd /\n", + " 13 cat ~.condarc\n", + " 14 nano ~/.condarc\n", + " 15 cat ~/.condarc\n", + " 16 module load Anaconda3\n", + " 17 conda create --name info302 python=3.7\n", + " 18 nano ~/.condarc \n", + " 19 conda create --name info302 python=3.7\n", + " 20 pip3 install bash_kernel\n", + " 21 python -m bash_kernel.install\n", + " 22 https://raw.githubusercontent.com/cb2edu/info302/2021/01-Linux_101/bash_class_assignment.ipynb\n", + " 23 wget https://raw.githubusercontent.com/cb2edu/info302/2021/01-Linux_101/bash_class_assignment.ipynb\n", + " 24 ls\n", + " 25 pwd\n", + " 26 cd\n", + " 27 ls\n", + " 28 wget https://raw.githubusercontent.com/cb2edu/info302/2021/01-Linux_101/bash_class_assignment.ipynb\n", + " 29 w get https://raw.githubusercontent.com/cb2edu/info302/2021/03-Reproducible_research/git_practicals.ipynb\n", + " 30 wget w get https://raw.githubusercontent.com/cb2edu/info302/2021/03-Reproducible_research/git_practicals.ipynb\n", + " 31 cd ~\n", + " 32 cd /mnt\n", + " 33 wget https://github.com/cb2edu/CB2-101-BioComp/raw/2020/01-Linux_101/data/linux_data.tar.xz.partaa\n", + " 34 wget https://github.com/cb2edu/CB2-101-BioComp/raw/2020/01-Linux_101/data/linux_data.tar.xz.partab\n", + " 35 ls\n", + " 36 cd\n", + " 37 cat linux_data.tar.xz.parta* > linux_data.tar.xz\n", + " 38 ls\n", + " 39 git clone $gitrepo test_class\n", + " 40 git clone $gitrepo testgit\n", + " 41 mkdir info302\n", + " 42 cd info302/\n", + " 43 pwd\n", + " 44 wget https://raw.githubusercontent.com/cb2edu/info302/2021/01-Linux_101/bash_class_assignment.ipynb\n", + " 45 wget https://raw.githubusercontent.com/cb2edu/info302/2021/03-Reproducible_research/git_practicals.ipynb\n", + " 46 git clone https://github.com/trinleb/info302_assignment.git\n", + " 47 ls\n", + " 48 info302_assignment//\n", + " 49 info 302_assignment/\n", + " 50 wget https://raw.githubusercontent.com/cb2edu/info302/2021/03-Reproducible_research/git_practicals.ipynb\n", + " 51 git status\n", + " 52 ls\n", + " 53 cd info302_assignment/\n", + " 54 ls\n", + " 55 git staus\n", + " 56 git status\n", + " 57 cp ../bash_class_assignment.ipynb .\n", + " 58 ls\n", + " 59 git status\n", + " 60 git add .-A\n", + " 61 git add . -A\n", + " 62 git status\n", + " 63 ls -la\n", + " 64 git commit -m \"First commit\"\n", + " 65 git push origin main\n", + " 66 ssh-keygen \n", + " 67 cd ~/.ssh/\n", + " 68 ls\n", + " 69 cat id rsa.pub\n", + " 70 cat id_rsa.pub\n", + " 71 ls\n", + " 72 cd\n", + " 73 cd info302/\n", + " 74 ls\n", + " 75 cd info302_assignment/\n", + " 76 ls\n", + " 77 mv info302_assignment_bak\n", + " 78 ls\n", + " 79 mv info_302_assignment info_302_assignment.bak\n", + " 80 cd..\n", + " 81 cd ..\n", + " 82 ls\n", + " 83 mv info302_assignment/ info302_assignment info302_assignment/.bak\n", + " 84 git clone git@github.com:trinleb/info302_assignment.git\n", + " 85 ls\n", + " 86 mv info302_assignment info_302_assignment.bak\n", + " 87 cd\n", + " 88 ls\n", + " 89 git clone git@github.com:trinleb/info302_assignment.git\n", + " 90 ls\n", + " 91 cp info302_assignment.bak/bash_class_assignment.ipynb info302_assignment/\n", + " 92 ls\n", + " 93 cd info302_assignment/\n", + " 94 ls\n", + " 95 cp ../bash_class_assignment.ipynb .\n", + " 96 ls\n", + " 97 git status\n", + " 98 git add . -A\n", + " 99 git commit -m \"first commit\"\n", + " 100 git push origin main\n", + " 101 less Encode-hesc-Nanog.bed\n", + " 102 cd linux_data/\n", + " 103 cd genomics_data/\n", + " 104 less Encode-hesc-Nanog.bed\n", + " 105 cd\n", + " 106 cd linux_data\n", + " 107 cd other\n", + " 108 vim listing.sh\n", + " 109 cd\n", + " 110 cd linux_data\n", + " 111 cd other\n", + " 112 vim listing.sh\n", + " 113 head -n 4 $file\n", + " 114 grep normal $meta\n", + " 115 cd\n", + " 116 cd linux_data\n", + " 117 cd other\n", + " 118 vim listing.sh\n", + " 119 PS1='[PEXP\\[\\]ECT_PROMPT>' PS2='[PEXP\\[\\]ECT_PROMPT+' PROMPT_COMMAND=''\n", + " 120 export PAGER=cat\n", + " 121 display () { TMPFILE=$(mktemp ${TMPDIR-/tmp}/bash_kernel.XXXXXXXXXX); cat > $TMPFILE; echo \"bash_kernel: saved image data to: $TMPFILE\" >&2; }\n", + " 122 cd\n", + " 123 cd linux_data\n", + " 124 cd other\n", + " 125 vim listing.sh\n", + " 126 PS1='[PEXP\\[\\]ECT_PROMPT>' PS2='[PEXP\\[\\]ECT_PROMPT+' PROMPT_COMMAND=''\n", + " 127 export PAGER=cat\n", + " 128 display () { TMPFILE=$(mktemp ${TMPDIR-/tmp}/bash_kernel.XXXXXXXXXX); cat > $TMPFILE; echo \"bash_kernel: saved image data to: $TMPFILE\" >&2; }\n", + " 129 cd\n", + " 130 echo $?\n", + " 131 pwd\n", + " 132 echo $?\n", + " 133 wget https://github.com/cb2edu/CB2-101-BioComp/raw/2020/01-Linux_101/data/linux_data.tar.xz.partaa\n", + " 134 wget https://github.com/cb2edu/CB2-101-BioComp/raw/2020/01-Linux_101/data/linux_data.tar.xz.partab\n", + " 135 echo $?\n", + " 136 ls\n", + " 137 echo $?\n", + " 138 cat linux_data.tar.xz.parta* > linux_data.tar.xz\n", + " 139 ls\n", + " 140 echo $?\n", + " 141 rm linux_data.tar.xz.parta*\n", + " 142 echo $?\n", + " 143 tar -xvJf linux_data.tar.xz\n", + " 144 echo $?\n", + " 145 ls\n", + " 146 echo $?\n", + " 147 cd linux_data\n", + " 148 cd reference_data\n", + " 149 ls\n", + " 150 echo $?\n", + " 151 cd linux_data\n", + " 152 mkdir selected_fastq\n", + " 153 echo $?\n", + " 154 pwd\n", + " 155 cd\n", + " 156 cd linux_data\n", + " 157 cd raw_fastq\n", + " 158 ls\n", + " 159 cp Irrel_kd_2.subset.fq /home/trinleb/linux_data/selected_fastq\n", + " 160 cp Mov10_oe_2.subset.fq /home/trinleb/linux_data/selected_fastq\n", + " 161 ls\n", + " 162 echo $?\n", + " 163 cd\n", + " 164 cd linux_data\n", + " 165 mv selected_fastq exercise1\n", + " 166 echo $?\n", + " 167 ls /usr/bin/c*\n", + " 168 ls /usr/bin/*a*\n", + " 169 ls /usr/bin/*o\n", + " 170 ls /usr/bin/*[ac]*\n", + " 171 echo $?\n", + " 172 history\n" + ] + } + ], + "source": [ + "history\n", + "# 279 commands\n", + "# the up arrow makes sense, it shows the previous command\n", + "# yes, Ctrl + C kills" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Files\n", + "\n", + "**Do the following in the terminal**\n", + "\n", + "1. Change directories into genomics_data. You can do this using a full or relative path.\n", + "2. Use the less command to open up the file Encode-hesc-Nanog.bed.\n", + "3. Search for the string chr11; you'll see all instances in the file highlighted.\n", + "4. Staying in the less buffer, use the shortcut to get to the end of the file. \n", + "5. Exit the less buffer and come back to the command prompt.\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Searching files\n", + "\n", + "1. Using `find` command search for the sequence file `Mov10_oe_1.subset.fq`.\n", + "2. Search for the sequence CTCAATGAGCCA in Mov10_oe_1.subset.fq. How many sequences do you find?\n", + "3. If you want to search for that sequence in **all** Mov10 replicate fastq files, what command would you use?\n" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "./raw_fastq/Mov10_oe_1.subset.fq\n", + "Irrel_kd_1.subset.fq Irrel_kd_3.subset.fq Mov10_oe_2.subset.fq\n", + "Irrel_kd_2.subset.fq Mov10_oe_1.subset.fq Mov10_oe_3.subset.fq\n", + "GGGTTGCCAATATTCACAGGACTATCTTCTTCCCAAGTTCACAATATGAGCCAACCAAAAATACTTTTGTCCCATACTCAATGAGCCAGTAAACAACTAG\n", + "CTCAATGAGCCAGTAAACAACTAGGCGGGCACAGGCAAAAACAATTTAGATAAATTTGACACCCCACCTCCTTTTTTTTTGTTCGAATTCTGGCTCCCTC\n", + "CAAGTTCACAATATGAGCCAACCAAAAATACTTTTGTCCCATACTCAATGAGCCAGTAAACAACTAGGCGGGCCCAGGCAAAAACAATTTAGATAAATTT\n", + "GCCAATATTCACAGGACTATCTTCTTCCCAAGTTCACAATATGAGCCAACCAAAAATACTTTTGTCCCATACTCAATGAGCCAGTAAACAACTAGGCGGG\n", + "GGAGATTCCAGCCAGGCTCTCAATGAGCCAGCAGAAGCAGCACTAAAGGACAGTGGAGGACTGACTGCCCTTGAGGGCAAGGAGGCCAGATCGGAAGAGC\n", + "Mov10_oe_1.subset.fq:GGGTTGCCAATATTCACAGGACTATCTTCTTCCCAAGTTCACAATATGAGCCAACCAAAAATACTTTTGTCCCATACTCAATGAGCCAGTAAACAACTAG\n", + "Mov10_oe_1.subset.fq:CTCAATGAGCCAGTAAACAACTAGGCGGGCACAGGCAAAAACAATTTAGATAAATTTGACACCCCACCTCCTTTTTTTTTGTTCGAATTCTGGCTCCCTC\n", + "Mov10_oe_1.subset.fq:CAAGTTCACAATATGAGCCAACCAAAAATACTTTTGTCCCATACTCAATGAGCCAGTAAACAACTAGGCGGGCCCAGGCAAAAACAATTTAGATAAATTT\n", + "Mov10_oe_1.subset.fq:GCCAATATTCACAGGACTATCTTCTTCCCAAGTTCACAATATGAGCCAACCAAAAATACTTTTGTCCCATACTCAATGAGCCAGTAAACAACTAGGCGGG\n", + "Mov10_oe_1.subset.fq:GGAGATTCCAGCCAGGCTCTCAATGAGCCAGCAGAAGCAGCACTAAAGGACAGTGGAGGACTGACTGCCCTTGAGGGCAAGGAGGCCAGATCGGAAGAGC\n", + "Mov10_oe_2.subset.fq:CCCAAGTTCACAATATGAGCCAACCAAAAATACTTTTGTCCCATACTCAATGAGCCAGTAAACAACTAGGCGGGCACAGGCAAAAACAATTTAGATAAAT\n", + "Mov10_oe_2.subset.fq:GAGCCAACCAAAAATACTTTTGTCCCATACTCAATGAGCCAGTAAACAACTAGGCGGGCACAGGCAAAAACAATTTAGATAAATTTGACACCCCATCTCC\n", + "Mov10_oe_2.subset.fq:CCCATACTCAATGAGCCAGTAAACAACTAGGCGGGCACAGGCAAAAACAATTTAGATAAATTTGACACCCCACCTCCTTTTTTTTTGTTCGAATTCTGGC\n" + ] + } + ], + "source": [ + "cd\n", + "cd linux_data\n", + "find . -name Mov10_oe_1.subset.fq\n", + "cd raw_fastq\n", + "ls\n", + "grep CTCAATGAGCCA Mov10_oe_1.subset.fq\n", + "grep CTCAATGAGCCA Mov10*\n", + "#5 sequences" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Searching and redirection\n", + "\n", + "How many unique exons are present on chromosome 1 using chr1-hg19_genes.gtf?\n", + "\n", + "1. Extract only the genomic coordinates of exon features\n", + "2. Subset dataset to only keep genomic coordinates\n", + "3. Remove duplicate exons\n", + "4. Count the total number of exons" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "chr1\tunknown\texon\t14362\t14829\t.\t-\t.\tgene_id \"WASH7P\"; gene_name \"WASH7P\"; transcript_id \"NR_024540\"; tss_id \"TSS7245\";\n", + "chr1\tunknown\texon\t14970\t15038\t.\t-\t.\tgene_id \"WASH7P\"; gene_name \"WASH7P\"; transcript_id \"NR_024540\"; tss_id \"TSS7245\";\n", + "chr1\tunknown\texon\t15796\t15947\t.\t-\t.\tgene_id \"WASH7P\"; gene_name \"WASH7P\"; transcript_id \"NR_024540\"; tss_id \"TSS7245\";\n", + "chr1\tunknown\texon\t16607\t16765\t.\t-\t.\tgene_id \"WASH7P\"; gene_name \"WASH7P\"; transcript_id \"NR_024540\"; tss_id \"TSS7245\";\n", + "chr1\tunknown\texon\t16858\t17055\t.\t-\t.\tgene_id \"WASH7P\"; gene_name \"WASH7P\"; transcript_id \"NR_024540\"; tss_id \"TSS7245\";\n", + "chr1\tunknown\texon\t17233\t17368\t.\t-\t.\tgene_id \"WASH7P\"; gene_name \"WASH7P\"; transcript_id \"NR_024540\"; tss_id \"TSS7245\";\n", + "chr1\tunknown\texon\t17606\t17742\t.\t-\t.\tgene_id \"WASH7P\"; gene_name \"WASH7P\"; transcript_id \"NR_024540\"; tss_id \"TSS7245\";\n", + "chr1\tunknown\texon\t17915\t18061\t.\t-\t.\tgene_id \"WASH7P\"; gene_name \"WASH7P\"; transcript_id \"NR_024540\"; tss_id \"TSS7245\";\n", + "chr1\tunknown\texon\t18268\t18366\t.\t-\t.\tgene_id \"WASH7P\"; gene_name \"WASH7P\"; transcript_id \"NR_024540\"; tss_id \"TSS7245\";\n", + "chr1\tunknown\texon\t24738\t24891\t.\t-\t.\tgene_id \"WASH7P\"; gene_name \"WASH7P\"; transcript_id \"NR_024540\"; tss_id \"TSS7245\";\n", + "grep: write error\n", + "chr1\t14362\t14829\t-\n", + "chr1\t14970\t15038\t-\n", + "chr1\t15796\t15947\t-\n", + "chr1\t16607\t16765\t-\n", + "chr1\t16858\t17055\t-\n", + "chr1\t17233\t17368\t-\n", + "chr1\t17606\t17742\t-\n", + "chr1\t17915\t18061\t-\n", + "chr1\t18268\t18366\t-\n", + "chr1\t24738\t24891\t-\n", + "cut: write error: Broken pipe\n", + "chr1\t10002682\t10002826\t-\n", + "chr1\t10003486\t10003573\t+\n", + "chr1\t100111431\t100111918\t+\n", + "chr1\t100127875\t100127955\t+\n", + "chr1\t100133198\t100133322\t+\n", + "chr1\t100152232\t100152346\t+\n", + "chr1\t100152486\t100152519\t+\n", + "chr1\t100152632\t100152745\t+\n", + "chr1\t100154331\t100155428\t+\n", + "chr1\t100154611\t100154621\t-\n", + "sort: write failed: standard output: Broken pipe\n", + "sort: write error\n", + "37213\n", + "22769\n" + ] + } + ], + "source": [ + "cd\n", + "cd linux_data\n", + "cd reference_data\n", + "grep exon chr1-hg19_genes.gtf | head\n", + "grep exon chr1-hg19_genes.gtf | cut -f1,4,5,7 | head\n", + "grep exon chr1-hg19_genes.gtf | cut -f1,4,5,7 | sort -u | head \n", + "grep exon chr1-hg19_genes.gtf | cut -f1,4,5,7 | wc -l\n", + "grep exon chr1-hg19_genes.gtf | cut -f1,4,5,7 | sort -u | wc -l\n", + "#22769" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Shell scripts\n", + "\n", + "1. Write a script `listing.sh`. Add the command which prints to screen the contents of the file `Mov10_rnaseq_metadata.txt`.\n", + "2. Add an echo statement for the command, which tells the user \"This is information about the files in our dataset:\"\n", + "3. Run the new script. Report the contents of the new script and the output you got after running it." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[24;1HE576: viminfo: Missing '>' in line: +^I7^I13\r\n" + ] + } + ], + "source": [ + "cd\n", + "cd linux_data\n", + "cd other\n", + "vim listing.sh\n", + "cat Mov10_rnaseq_metadata.txt\n", + "echo \"This is information about the files in our dataset:\"\n", + "sh listing.sh" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + " ## Bash variables\n", + "\n", + "1. Use the `$file` variable as input to the head and tail commands, and modify the arguments to display only four lines from any file. \n", + "2. Create a new variable called meta and assign it the value Mov10_rnaseq_metadata.txt. For the following questions, use the $meta variable but do not change directories. Provide the code you would run to:\n", + " \n", + " a. Display the contents of the file using cat.\n", + " b. Retrieve only the lines which contain normal samples. (Hint: use grep)" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\r\n" + ] + } + ], + "source": [ + "head -n 4 $file\n", + "meta=Mov10_rnaseq_metadata.txt\n", + "cat $meta\n", + "grep normal $meta\n", + "# IR.1 normal\n", + "# IR.2 normal\n", + "# IR.3 normal" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + " \n", + "## Filename\n", + "\n", + "1. How would you modify basename command above to only return Mov10_oe_1 from the filename `Mov10_oe_1.subset.fq`?\n", + "2. Use basename with the file Irrel_kd_1.subset.fq as input. Return only Irrel_kd_1 to the terminal." + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Mov10_oe_1\n", + "Irrel_kd_1\n" + ] + } + ], + "source": [ + "basename ~/linux_data/raw_fastq/Mov10_oe_1.subset.fq .subset.fq\n", + "basename ~/linux_data/raw_fastq/Irrel_kd_1.subset.fq .subset.fq" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## `for` loop\n", + "\n", + "Write a loop to print out the number of lines in each fasta file in the dataset. The output should look something like this:\n", + "```\n", + " Irrel_kd_1.subset.fq 891684\n", + " Irrel_kd_2.subset.fq 767072\n", + " Irrel_kd_3.subset.fq 586196\n", + " Mov10_oe_1.subset.fq 1223600\n", + " Mov10_oe_2.subset.fq 1110016\n", + " Mov10_oe_3.subset.fq 690816\n", + "```" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "135753\n", + "116598\n", + "88359\n", + "184391\n", + "167773\n", + "102921\n" + ] + } + ], + "source": [ + "cd\n", + "cd linux_data\n", + "cd raw_fastq\n", + "grep -c \">\" Irrel_kd_1.subset.fq\n", + "grep -c \">\" Irrel_kd_2.subset.fq\n", + "grep -c \">\" Irrel_kd_3.subset.fq\n", + "grep -c \">\" Mov10_oe_1.subset.fq\n", + "grep -c \">\" Mov10_oe_2.subset.fq\n", + "grep -c \">\" Mov10_oe_3.subset.fq" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Bash", + "language": "bash", + "name": "bash" + }, + "language_info": { + "codemirror_mode": "shell", + "file_extension": ".sh", + "mimetype": "text/x-sh", + "name": "bash" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +}