Mercurial > repos > brinkmanlab > biopython_convert
changeset 4:a5cb5e374399 draft
"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 | d9ae46bb9f09 |
| children | 1c71c770bfd4 |
| files | bioperl_compat.py |
| diffstat | 1 files changed, 15 insertions(+), 1 deletions(-) [+] |
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--- a/bioperl_compat.py Tue Nov 10 21:14:06 2020 +0000 +++ b/bioperl_compat.py Thu Feb 04 01:30:20 2021 +0000 @@ -1,11 +1,25 @@ #!/usr/bin/env python import sys from biopython_convert import get_args, convert -from Bio.SeqIO.InsdcIO import _InsdcWriter +from Bio.SeqIO.InsdcIO import _InsdcWriter, EmblWriter +import Bio # Quote anticodon qualifiers _InsdcWriter.FTQUAL_NO_QUOTE = tuple(v for v in _InsdcWriter.FTQUAL_NO_QUOTE if v not in ['anticodon', 'transl_except']) +if Bio.__version__ == "1.78": + # TODO monkeypatch until https://github.com/biopython/biopython/pull/3476 + _write_the_first_lines_orig = EmblWriter._write_the_first_lines + + def _write_the_first_lines(self, record): + orig_type = record.annotations.get("molecule_type") + record.annotations["molecule_type"] = orig_type.upper() + ret = _write_the_first_lines_orig(self, record) + record.annotations["molecule_type"] = orig_type + return ret + + EmblWriter._write_the_first_lines = _write_the_first_lines + if __name__ == '__main__': convert(*get_args(sys.argv[1:]))