Mercurial > repos > brinkmanlab > biopython_convert
annotate bioperl_compat.py @ 3:d9ae46bb9f09 draft
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 9daa118327386dc1104febd656b57cb8b8dde1e9"
author | brinkmanlab |
---|---|
date | Tue, 10 Nov 2020 21:14:06 +0000 |
parents | 869e206b3ca1 |
children | a5cb5e374399 |
rev | line source |
---|---|
0
869e206b3ca1
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff
changeset
|
1 #!/usr/bin/env python |
869e206b3ca1
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff
changeset
|
2 import sys |
869e206b3ca1
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff
changeset
|
3 from biopython_convert import get_args, convert |
869e206b3ca1
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff
changeset
|
4 from Bio.SeqIO.InsdcIO import _InsdcWriter |
869e206b3ca1
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff
changeset
|
5 |
869e206b3ca1
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff
changeset
|
6 # Quote anticodon qualifiers |
869e206b3ca1
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff
changeset
|
7 _InsdcWriter.FTQUAL_NO_QUOTE = tuple(v for v in _InsdcWriter.FTQUAL_NO_QUOTE if v not in ['anticodon', 'transl_except']) |
869e206b3ca1
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff
changeset
|
8 |
869e206b3ca1
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff
changeset
|
9 if __name__ == '__main__': |
869e206b3ca1
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff
changeset
|
10 convert(*get_args(sys.argv[1:])) |
869e206b3ca1
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff
changeset
|
11 |