initial commit of genbank script

CHANGELOG.rst

@@ -2,6 +2,11 @@
 CHANGELOG
 =========
 
+Version 1.4.0
+-------------
+
+* added genbank downloader script
+
 Version 1.3.2
 -------------
 

bio_bits/genbank.py

@@ -0,0 +1,45 @@
+'''
+Usage:
+  genbank <infile>
+'''
+from Bio import SeqIO
+import dateparser
+import sys
+from docopt import docopt
+
+def rec_qualifier(rec, key):
+  for f in rec.features:
+    if f.qualifiers:
+      if 'collection_date' in f.qualifiers:
+        return f.qualifiers[key]
+
+def fix_date(d):
+    date = dateparser.parse(d)
+    return date.strftime('%Y-%m-%d')
+
+def rec_to_fasta(rec):
+  raw_collection_date = rec_qualifier(rec, 'collection_date')[0]
+  country = rec_qualifier(rec, 'country')[0]
+  date = dateparser.parse(raw_collection_date)
+  date = date.strftime('%Y-%m-%d')
+  rec.description = "|{}|{}".format(country, date)
+  return rec
+
+  # acc = rec.name
+  #header = "{}|{}|{}".format(acc, country, date)
+  #seq = str(rec.seq)
+  #return rec.format("fasta")
+def run(infile):
+  with open(infile) as input:
+    gb = SeqIO.parse(input, 'genbank')
+    results = map(rec_to_fasta, gb)
+    SeqIO.write(results, sys.stdout, 'fasta')
+
+def main():
+  raw_args = docopt(__doc__, version='Version 1.0')
+  run(raw_args['<infile>'])
+  sys.exit(0)
+
+
+# ['17-Feb-2010']
+# rec = degen.id_to_record("KJ627355")

requirements-pip.txt

@@ -1,5 +1,6 @@
 argparse
 docopt
+dateparser
 future
 schema
 sh

setup.py

@@ -27,6 +27,7 @@
             'degen = bio_bits.degen:main',
             'plot_muts = bio_bits.plot_muts:main',
             'fasta = bio_bits.fasta:main',
+            'genbank = bio_bits.genbank:main',
             #'sequence_concat = bio_bits.sequence_concat:main',
             #'sequence_files_concat = bio_bits.sequence_files_concat:main',
             #'sequence_split = bio_bits_old.sequence_split:main',