obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

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

Browse Source 
view type
This commit is contained in:
Celine Mercier
2019-09-17 13:22:41 +02:00
parent 9063e9159d
commit ad46056179
1 changed files with 11 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
python/obitools3/commands/export.pyx
View File

@ -5,6 +5,7 @@ from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger
from obitools3.dms import DMS
from obitools3.dms.obiseq import Nuc_Seq
from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
from obitools3.apps.optiongroups import addMinimalInputOption, \
addExportOutputOption, \
@ -35,6 +36,15 @@ def run(config):
raise Exception("Could not read input")
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
output = open_uri(config['obi']['outputURI'],
input=False)