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annotate 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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f6d6b62540f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
rnateam
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1 #!/usr/bin/env python
f6d6b62540f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
rnateam
parents:
diff changeset
2 import os
f6d6b62540f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
rnateam
parents:
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3 import sys
f6d6b62540f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
rnateam
parents:
diff changeset
4 from Bio import SeqIO
f6d6b62540f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
rnateam
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5
f6d6b62540f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
rnateam
parents:
diff changeset
6 if __name__ == "__main__":
f6d6b62540f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
rnateam
parents:
diff changeset
7 inpath = sys.argv[1]
f6d6b62540f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
rnateam
parents:
diff changeset
8 os.mkdir('splits')
f6d6b62540f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
rnateam
parents:
diff changeset
9 with open(inpath, 'r') as handle:
f6d6b62540f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
rnateam
parents:
diff changeset
10 for record in SeqIO.parse(handle, 'fasta'):
f6d6b62540f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
rnateam
parents:
diff changeset
11 header = os.path.join('splits', record.id + '.fasta')
f6d6b62540f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
rnateam
parents:
diff changeset
12 with open(header, 'w') as handle2:
f6d6b62540f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta commit 03f3cc2000e6ce876a3cb44c55c3fe878a2e7ce3-dirty
rnateam
parents:
diff changeset
13 SeqIO.write([record], handle2, 'fasta')