From ad46056179a91c287c02a5ecad7c65629221e414 Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Tue, 17 Sep 2019 13:22:41 +0200 Subject: [PATCH] obi export: if export format is not specified, it is guessed from the view type --- python/obitools3/commands/export.pyx | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/python/obitools3/commands/export.pyx b/python/obitools3/commands/export.pyx index 8fe7df1..2f5e354 100755 --- a/python/obitools3/commands/export.pyx +++ b/python/obitools3/commands/export.pyx @@ -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, \ @@ -34,7 +35,16 @@ def run(config): if input is None: 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)