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obi export: if export format is not specified, it is guessed from the

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Celine Mercier
2019-09-17 13:22:41 +02:00
parent 9063e9159d
commit ad46056179
1 changed files with 11 additions and 1 deletions
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12
python/obitools3/commands/export.pyx
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@ -5,6 +5,7 @@ from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger from obitools3.apps.config import logger
from obitools3.dms import DMS from obitools3.dms import DMS
from obitools3.dms.obiseq import Nuc_Seq from obitools3.dms.obiseq import Nuc_Seq
from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
from obitools3.apps.optiongroups import addMinimalInputOption, \ from obitools3.apps.optiongroups import addMinimalInputOption, \
addExportOutputOption, \ addExportOutputOption, \
@ -34,7 +35,16 @@ def run(config):
if input is None: if input is None:
raise Exception("Could not read input") raise Exception("Could not read input")
iview = input[1] iview = input[1]
if 'outputformat' not in config['obi']:
if iview.type == b"NUC_SEQS_VIEW":
if QUALITY_COLUMN in iview:
config['obi']['outputformat'] = b'fastq'
else:
config['obi']['outputformat'] = b'fasta'
else:
config['obi']['outputformat'] = b'tabular'
# Open the output # Open the output
output = open_uri(config['obi']['outputURI'], output = open_uri(config['obi']['outputURI'],
input=False) input=False)