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Added properties for Nuc_Seq cython classes (and updated commands using

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them)
This commit is contained in:
Celine Mercier
2016-11-08 16:59:32 +01:00
parent b5b889c4a2
commit 51b23915ca
4 changed files with 89 additions and 90 deletions
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6
python/obitools3/commands/export.pyx
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@ -67,16 +67,16 @@ def run(config):
for seq in iview :
pb(i)
toprint = ">"+seq.get_id()+" "
toprint = ">"+seq.id+" "
for col_name in seq :
if col_name not in special_columns :
toprint = toprint + col_name + "=" + str(seq[col_name]) + "; "
if DEFINITION_COLUMN in seq :
toprint = toprint + seq.get_definition()
toprint = toprint + seq.definition
nucseq = bytes2str(seq.get_sequence())
nucseq = bytes2str(seq.nuc_seq)
if config['export']['format'] == "fasta" :
nucseq = re.sub("(.{60})", "\\1\n", nucseq, 0, re.DOTALL)