fixed biopython deprecation warning

Author: Tobias Hofmann

build/lib/secapr/_version.py

@@ -8,11 +8,11 @@
 
 version_json = '''
 {
- "date": "2020-09-03T08:40:33+0200",
+ "date": "2020-09-03T14:47:02+0200",
  "dirty": true,
  "error": null,
- "full-revisionid": "6c64e8334194adde121523290caf950c97360619",
- "version": "1.1.12+43.g6c64e83.dirty"
+ "full-revisionid": "0e245431fefa2d8aab32a86e62516b151dee55e4",
+ "version": "1.1.12+44.g0e24543.dirty"
 }
 '''  # END VERSION_JSON
 

build/lib/secapr/align_sequences.py

@@ -164,7 +164,8 @@ def create_locus_specific_fasta(sequences):
     #fd, fasta_file = tempfile.mkstemp()
     handle = open(fasta_file,'w')
     for seq in sequences:
-        handle.write(seq.format("fasta"))
+        seq.id = '_'.join(seq.id.split('_')[1:])
+        handle.write(format(seq,"fasta"))
     return fasta_file
 
 

build/lib/secapr/helpers.py

@@ -274,17 +274,17 @@ def get_alignment_files(log, input_dir, input_format):
     return alignments
 
 
-def write_alignments_to_outdir(log, outdir, alignments, format):
+def write_alignments_to_outdir(log, outdir, alignments, alformat):
     log.info('Writing output files')
     for tup in alignments:
         locus, aln = tup
         if aln.trimmed is not None:
             outname = "{}{}".format(
                 os.path.join(outdir, locus),
-                get_file_extensions(format)[0]
+                get_file_extensions(alformat)[0]
             )
             with open(outname, 'w') as outf:
-                outf.write(aln.trimmed.format(format))
+                outf.write(format(aln.trimmed,alformat))
         else:
             log.warn("DROPPED {0} from output".format(locus))
 

dist/secapr-1.1.12+44.g0e24543-py3.8.egg

@@ -0,0 +1,50 @@
+{% set version = "1.1.15" %}
+
+package:
+  name: secapr
+  version: {{ version }}
+
+source:
+  url: https://github.com/AntonelliLab/seqcap_processor/archive/v{{ version }}.tar.gz
+  sha256: 0bf985591b8c44f69ca1d4c40d0d37c871d914336d1846a70cad209fcab529c1
+
+build:
+  skip: True  # [not py27] 
+  number: 0
+  script: python -m pip install --no-deps --ignore-installed .
+  entry_points:
+    - secapr = secapr.__main__:main
+
+requirements:
+  host:
+    - python
+    - pip
+    - setuptools
+
+  run:
+    - python
+    - pandas
+    - matplotlib
+    - biopython
+    - trimmomatic
+    - fastqc
+    - abyss
+    - spades
+    - blast
+    - mafft
+    - muscle
+    - emboss
+    - bwa
+    - samtools
+
+test:
+  imports:
+    - secapr
+  commands:
+    - secapr --version
+
+about:
+  home: 'https://github.com/AntonelliLab/seqcap_processor'
+  license: MIT
+  license_file: LICENSE
+  summary: 'Process sequence-capture FASTQ files into alignments for phylogenetic analyses. Integrates allele phasing, producing haplotype alignments.'

dist/secapr-1.1.12+44.g0e24543.dirty-py3.8.egg

@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: secapr
-Version: 1.1.12+43.g6c64e83.dirty
+Version: 1.1.12+44.g0e24543.dirty
 Summary: Process sequence-capture fastq files into alignments for phylogenetic analyses
 Home-page: https://github.com/AntonelliLab/seqcap_processor
 Author: Tobias Andermann

recipe/meta.yaml

@@ -164,7 +164,8 @@ def create_locus_specific_fasta(sequences):
     #fd, fasta_file = tempfile.mkstemp()
     handle = open(fasta_file,'w')
     for seq in sequences:
-        handle.write(seq.format("fasta"))
+        seq.id = '_'.join(seq.id.split('_')[1:])
+        handle.write(format(seq,"fasta"))
     return fasta_file
 
 

secapr.egg-info/PKG-INFO

@@ -274,17 +274,17 @@ def get_alignment_files(log, input_dir, input_format):
     return alignments
 
 
-def write_alignments_to_outdir(log, outdir, alignments, format):
+def write_alignments_to_outdir(log, outdir, alignments, alformat):
     log.info('Writing output files')
     for tup in alignments:
         locus, aln = tup
         if aln.trimmed is not None:
             outname = "{}{}".format(
                 os.path.join(outdir, locus),
-                get_file_extensions(format)[0]
+                get_file_extensions(alformat)[0]
             )
             with open(outname, 'w') as outf:
-                outf.write(aln.trimmed.format(format))
+                outf.write(format(aln.trimmed,alformat))
         else:
             log.warn("DROPPED {0} from output".format(locus))