Mercurial > repos > peterjc > align_back_trans

comparison tools/align_back_trans/align_back_trans.py @ 6:b27388e5a0bb draft

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v0.0.10 removed unused reference to muscle format
author peterjc
date Mon, 21 Aug 2017 06:26:14 -0400
parents 2c32e8a8990f
children 883842b81796
comparison
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5:2c32e8a8990f 6:b27388e5a0bb
86 sys.stderr.write("Translation: %s\n\n" % t[offset:offset + 60]) 86 sys.stderr.write("Translation: %s\n\n" % t[offset:offset + 60])
87 sys.exit("Translation check failed for %s\n" % identifier) 87 sys.exit("Translation check failed for %s\n" % identifier)
88 88
89 89
90 def sequence_back_translate(aligned_protein_record, unaligned_nucleotide_record, gap, table=0): 90 def sequence_back_translate(aligned_protein_record, unaligned_nucleotide_record, gap, table=0):
91 """Back-translate a sequence."""
91 # TODO - Separate arguments for protein gap and nucleotide gap? 92 # TODO - Separate arguments for protein gap and nucleotide gap?
92 if not gap or len(gap) != 1: 93 if not gap or len(gap) != 1:
93 raise ValueError("Please supply a single gap character") 94 raise ValueError("Please supply a single gap character")
94 95
95 alpha = unaligned_nucleotide_record.seq.alphabet 96 alpha = unaligned_nucleotide_record.seq.alphabet