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

ngsfilter: unidentified sequences are now stored untrimmed

Browse Source
This commit is contained in:
Celine Mercier
2020-07-13 15:56:40 +02:00
parent 9ace9989c4
commit ed9549acfb
1 changed files with 8 additions and 2 deletions
Download Patch File Download Diff File Expand all files Collapse all files

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

@ -58,7 +58,7 @@ def addOptions(parser):
metavar="<URI>", metavar="<URI>",
type=str, type=str,
default=None, default=None,
help="URI to the view used to store the sequences unassigned to any sample") help="URI to the view used to store the sequences unassigned to any sample. Those sequences are untrimmed.")
group.add_argument('--no-tags', group.add_argument('--no-tags',
action="store_true", dest="ngsfilter:notags", action="store_true", dest="ngsfilter:notags",
@ -646,7 +646,13 @@ def run(config):
o_view[g].set(oseq.id, oseq.seq, definition=oseq.definition, quality=oseq.quality, tags=oseq) o_view[g].set(oseq.id, oseq.seq, definition=oseq.definition, quality=oseq.quality, tags=oseq)
g+=1 g+=1
elif unidentified is not None: elif unidentified is not None:
unidentified[u].set(oseq.id, oseq.seq, definition=oseq.definition, quality=oseq.quality, tags=oseq) # Untrim sequences (put original back)
if len(modseq) > 1:
oseq[REVERSE_SEQUENCE_COLUMN] = reverse[i].seq
oseq[REVERSE_QUALITY_COLUMN] = reverse[i].quality
unidentified[u].set(oseq.id, forward[i].seq, definition=oseq.definition, quality=forward[i].quality, tags=oseq)
else:
unidentified[u].set(oseq.id, entries[i].seq, definition=oseq.definition, quality=entries[i].quality, tags=oseq)
u+=1 u+=1
except Exception, e: except Exception, e:
if unidentified is not None: if unidentified is not None: