Mercurial > repos > rnateam > splitfasta

diff splitFasta.py @ 0:f6d6b62540f8 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
author rnateam
date Fri, 16 Oct 2015 16:13:08 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/splitFasta.py	Fri Oct 16 16:13:08 2015 -0400
@@ -0,0 +1,13 @@
+#!/usr/bin/env python
+import os
+import sys
+from Bio import SeqIO
+
+if __name__ == "__main__":
+    inpath = sys.argv[1]
+    os.mkdir('splits')
+    with open(inpath, 'r') as handle:
+        for record in SeqIO.parse(handle, 'fasta'):
+            header = os.path.join('splits', record.id + '.fasta')
+            with open(header, 'w') as handle2:
+                SeqIO.write([record], handle2, 'fasta')