diff glimmer2seq.py @ 0:841357e0acbf draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer2seq.py	Sat Jul 06 10:09:30 2013 -0400
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+"""
+Input: DNA FASTA file + Glimmer ORF file
+Output: ORF sequences as FASTA file
+Author: Bjoern Gruening
+"""
+import sys, os
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
+
+def glimmer2seq( glimmer_prediction = sys.argv [1], genome_sequence = sys.argv[2], outfile = sys.argv[3] ):
+    if len(sys.argv) >= 4:
+        glimmerfile = open( glimmer_prediction, "r")
+        sequence = open( genome_sequence )
+    else:
+        print "Missing input values."
+        sys.exit()
+
+    fastafile = SeqIO.parse(sequence, "fasta")
+
+    sequences = dict()
+    seq_records = list()
+    for entry in fastafile:
+        sequences[entry.description] = entry
+
+    for line in glimmerfile:
+        if line.startswith('>'):
+            entry = sequences[ line[1:].strip() ]
+        else:
+            orf_start = int(line[8:17])
+            orf_end = int(line[18:26])
+
+            orf_name = line[0:8]
+            if orf_start <= orf_end:
+                seq_records.append( SeqRecord( entry.seq[ orf_start-1 : orf_end ], id = orf_name, description = entry.description ) )
+            else:
+                seq_records.append( SeqRecord( entry.seq[ orf_end-1 : orf_start ].reverse_complement(), id = orf_name, description = entry.description ) )
+
+    SeqIO.write( seq_records, outfile, "fasta" )
+    glimmerfile.close()
+    sequence.close()
+
+if __name__ == "__main__" :
+    glimmer2seq()