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Major update: New column type to store sequence qualities. Closes #41

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This commit is contained in:
Celine Mercier
2016-05-20 16:45:22 +02:00
parent ffff91e76c
commit 3b59043ea8
33 changed files with 962 additions and 267 deletions
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7
python/obitools3/commands/import.pyx
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@ -35,7 +35,6 @@ def addOptions(parser):
type=str,
help="Name of the default DMS for reading and writing data")
group.add_argument('--destination-view','-v',
action="store", dest="import:destview",
metavar='<VIEW NAME>',
@ -96,12 +95,14 @@ def run(config):
inputs = uopen(config['import']['filename'])
get_quality = False
if config['import']['seqinformat']=='fasta':
iseq = fastaIterator(inputs)
view_type="NUC_SEQS_VIEW"
elif config['import']['seqinformat']=='fastq':
iseq = fastqIterator(inputs)
view_type="NUC_SEQS_VIEW"
get_quality = True
else:
raise RuntimeError('No file format specified')
@ -120,13 +121,15 @@ def run(config):
view[i].set_id(seq['id'])
view[i].set_definition(seq['definition'])
view[i].set_sequence(seq['sequence'])
if get_quality :
view[i].set_quality(seq['quality'])
for tag in seq['tags'] :
#print(tag, seq['tags'][tag])
#if seq['tags'][tag] not in NA_list :
view[i][tag] = seq['tags'][tag]
i+=1
#print(view)
#print(i)
print(view.__repr__())
view.save_and_close()