diff glimmer2seq.py @ 0:3aa8a98be9a3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer2seq.py	Tue Nov 28 10:15:43 2017 -0500
@@ -0,0 +1,47 @@
+#!/usr/bin/env python
+"""
+Input: DNA FASTA file + Glimmer ORF file
+Output: ORF sequences as FASTA file
+Author: Bjoern Gruening
+"""
+import sys
+
+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()