Mercurial > repos > brinkmanlab > biopython_convert

annotate bioperl_compat.py @ 4:a5cb5e374399 draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
author brinkmanlab
date Thu, 04 Feb 2021 01:30:20 +0000
parents 869e206b3ca1
children
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869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
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1 #!/usr/bin/env python
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
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2 import sys
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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3 from biopython_convert import get_args, convert
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a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
brinkmanlab
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4 from Bio.SeqIO.InsdcIO import _InsdcWriter, EmblWriter
a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
brinkmanlab
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5 import Bio
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869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
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7 # Quote anticodon qualifiers
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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8 _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"
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a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
brinkmanlab
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10 if Bio.__version__ == "1.78":
a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
brinkmanlab
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11 # TODO monkeypatch until https://github.com/biopython/biopython/pull/3476
a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
brinkmanlab
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12 _write_the_first_lines_orig = EmblWriter._write_the_first_lines
a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
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a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
brinkmanlab
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14 def _write_the_first_lines(self, record):
a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
brinkmanlab
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15 orig_type = record.annotations.get("molecule_type")
a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
brinkmanlab
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16 record.annotations["molecule_type"] = orig_type.upper()
a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
brinkmanlab
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17 ret = _write_the_first_lines_orig(self, record)
a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
brinkmanlab
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18 record.annotations["molecule_type"] = orig_type
a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
brinkmanlab
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19 return ret
a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
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a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
brinkmanlab
parents: 0
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21 EmblWriter._write_the_first_lines = _write_the_first_lines
a5cb5e374399 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit afc9f4ade42686dcf53a2615d90e1e9962cf1561"
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869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
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23 if __name__ == '__main__':
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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24 convert(*get_args(sys.argv[1:]))
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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