New upstream version 2.9.3+ds
Sascha Steinbiss
7 years ago
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import tempfile
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import re
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import time
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import os
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import shutil
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def _rename_seqs_in_fasta(cls, infile, outfile):
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f = pyfastaq.utils.open_file_write(outfile)
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file_reader = pyfastaq.sequences.file_reader(infile)
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nodot_regex = re.compile(r'^.*(?P<separator>[^.0-9])[0-9]+$')
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for seq in file_reader:
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seq.id = seq.id.replace('_', '.').replace('-', '.')
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if seq.id.startswith('Oxf.'):
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seq.id = 'Oxf_' + seq.id[4:]
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regex_match = nodot_regex.match(seq.id)
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if regex_match is not None:
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seq.id = '.'.join(seq.id.rsplit(regex_match.groupdict()['separator'], maxsplit=1))
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print(seq, file=f)
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pyfastaq.utils.close(f)
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AAAA
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>gene.3
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CCCC
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>foo_gene.4
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TTTT
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>Oxf_gltA.42
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A
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>Oxf_gltA.43
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C
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>Oxf_gltA.44
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G
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>Oxf_gltA.45
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T
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AAAA
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>gene.3
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CCCC
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>foo_gene.4
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TTTT
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>Oxf.gltA.42
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A
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>Oxf.gltA-43
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C
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>Oxf.gltA_44
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G
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>Oxf.gltA?45
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T
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setup(
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ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
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name='ariba',
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version='2.9.2',
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version='2.9.3',
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description='ARIBA: Antibiotic Resistance Identification By Assembly',
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packages = find_packages(),
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package_data={'ariba': ['test_run_data/*']},
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