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Minor improvements to obi export command

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This commit is contained in:
Celine Mercier
2016-08-19 17:49:22 +02:00
parent b34769b27c
commit 8d360b0fac
1 changed files with 3 additions and 1 deletions
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4
python/obitools3/commands/export.pyx
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@ -48,6 +48,8 @@ def run(config):
DEFINITION_COLUMN = "DEFINITION" DEFINITION_COLUMN = "DEFINITION"
QUALITY_COLUMN = "QUALITY" QUALITY_COLUMN = "QUALITY"
special_columns = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
# Open DMS # Open DMS
d = OBIDMS(config['obi']['defaultdms']) d = OBIDMS(config['obi']['defaultdms'])
@ -64,7 +66,7 @@ def run(config):
toprint = ">"+seq.get_id()+" " toprint = ">"+seq.get_id()+" "
for col_name in seq : for col_name in seq :
if col_name != NUC_SEQUENCE_COLUMN and col_name != ID_COLUMN and col_name != DEFINITION_COLUMN and col_name != QUALITY_COLUMN : if col_name not in special_columns :
toprint = toprint + col_name + "=" + str(seq[col_name]) + "; " toprint = toprint + col_name + "=" + str(seq[col_name]) + "; "
if DEFINITION_COLUMN in seq : if DEFINITION_COLUMN in seq :