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New script (alpha).

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1 parent 105ab8f commit ab45864a87d7fe515e1505af906862390b349ddf @bl0b committed Aug 6, 2012
Showing with 12 additions and 0 deletions.
  1. +12 −0 convert_exonerate_to_fasta.py
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+#!/usr/bin/env python
+from parse_exonerate import Exonerate
+import sys
+from fasta import Sequence
+
+for filename in sys.argv[1:]:
+ e = Exonerate(filename)
+ out = open(filename + '.fas', 'w')
+ for q in e.queries:
+ s = Sequence(q.Query.split(' ')[0] + '_' + q.Target,
+ q.target_seq.replace('-', 'N'))
+ print >> out, s

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