diff gbk2fa.py @ 10:5b4ac70948d2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gbk2fa.py	Tue Mar 27 09:44:18 2018 -0400
@@ -0,0 +1,43 @@
+import argparse
+import bz2
+import contextlib
+import gzip
+import sys
+
+import magic
+from Bio import SeqIO
+
+parser = argparse.ArgumentParser()
+parser.add_argument("genbank_file", help="GenBank input file. Can be compressed with gzip or bzip2")
+parser.add_argument("fasta_file", help="FASTA output datset")
+parser.add_argument("--remove_version", dest="remove_version", action="store_true", help="Remove version number from NCBI form formatted accession numbers. For example, this would convert 'B000657.2' to 'B000657'")
+args = parser.parse_args()
+
+gbk_filename = args.genbank_file
+fa_filename = args.fasta_file
+
+
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+def get_file_handle(gbk_filename):
+    f_type = magic.from_file(args.genbank_file, mime=True)
+    if f_type == 'text/plain':
+        input_handle = open(gbk_filename, "r")
+    elif f_type == 'application/gzip':
+        input_handle = gzip.open(gbk_filename, "rt")
+    elif f_type == 'application/x-bzip2':
+        input_handle = bz2.open(gbk_filename, "rt")
+    else:
+        sys.exit("Cannot process file of type {}. Only plain, gzip'ed, and bzip2'ed genbank files are accepted ".format(f_type))
+    yield input_handle
+    input_handle.close()
+
+
+with get_file_handle(gbk_filename) as input_handle, open(fa_filename, "w") as output_handle:
+
+    for seq_record in SeqIO.parse(input_handle, "genbank"):
+        if args.remove_version:
+            seq_id = seq_record.id.split('.')[0]
+        else:
+            seq_id = seq_record.id
+        print('Writing FASTA record: {}'.format( seq_id ))
+        output_handle.write(">{}\n{}\n".format(seq_id, seq_record.seq))