Mercurial > repos > brinkmanlab > mauve_contig_mover

comparison stitch.py @ 4:71831ead9e16 draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit f3a482a9df3fd689699752cdd0751e83670e3b64"
author brinkmanlab
date Tue, 23 Jun 2020 15:54:29 -0400
parents c14690ec0c9f
children
comparison
equal deleted inserted replaced
3:38fbb67f0dac 4:71831ead9e16
126 126
127 if result and seqid: 127 if result and seqid:
128 result.id = seqid 128 result.id = seqid
129 result.description = "" 129 result.description = ""
130 130
131 seqlenlen = len(str(len(result)))
132 if len(result.id) + 1 + seqlenlen > 28:
133 # Genbank has a max length for the id and sequence length number, truncate the sequence id ov too long
134 result.id = result.id[:27 - seqlenlen]
135
136 result.seq.alphabet = Alphabet.generic_dna # TODO Investigate why this is required for some datasets 131 result.seq.alphabet = Alphabet.generic_dna # TODO Investigate why this is required for some datasets
137 SeqIO.write(result, sys.stdout, draft_format) 132 SeqIO.write(result, sys.stdout, draft_format)