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ngsfilter: now checking primer length (fixes #75)

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Celine Mercier
2020-04-05 18:29:10 +02:00
parent 8019dee68e
commit f0d152fcbd
1 changed files with 18 additions and 5 deletions
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23
python/obitools3/commands/ngsfilter.pyx
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@ -172,6 +172,13 @@ cdef read_info_view(info_view, max_errors=2, verbose=False, not_aligned=False):
primer_list = [] primer_list = []
i=0 i=0
for p in info_view: for p in info_view:
# Check primer length: should not be longer than 32, the max allowed by the apat lib
if len(p[b'forward_primer']) > 32:
raise RollbackException("Error: primers can not be longer than 32bp, rollbacking views")
if len(p[b'reverse_primer']) > 32:
raise RollbackException("Error: primers can not be longer than 32bp, rollbacking views")
forward=Primer(p[b'forward_primer'], forward=Primer(p[b'forward_primer'],
len(p[b'forward_tag']) if (b'forward_tag' in p and p[b'forward_tag']!=None) else None, len(p[b'forward_tag']) if (b'forward_tag' in p and p[b'forward_tag']!=None) else None,
True, True,
@ -594,7 +601,13 @@ def run(config):
pb = ProgressBar(entries_len, config, seconde=5) pb = ProgressBar(entries_len, config, seconde=5)
# Check and store primers and tags # Check and store primers and tags
infos, primer_list = read_info_view(info_view, max_errors=config['ngsfilter']['error'], verbose=False, not_aligned=not_aligned) # TODO obi verbose option try:
infos, primer_list = read_info_view(info_view, max_errors=config['ngsfilter']['error'], verbose=False, not_aligned=not_aligned) # TODO obi verbose option
except RollbackException, e:
if unidentified is not None:
raise RollbackException("obi ngsfilter error, rollbacking views: "+str(e), o_view, unidentified)
else:
raise RollbackException("obi ngsfilter error, rollbacking view: "+str(e), o_view)
aligner = Primer_search(primer_list, config['ngsfilter']['error']) aligner = Primer_search(primer_list, config['ngsfilter']['error'])
@ -652,11 +665,11 @@ def run(config):
#print("\n\nOutput view:\n````````````", file=sys.stderr) #print("\n\nOutput view:\n````````````", file=sys.stderr)
#print(repr(o_view), file=sys.stderr) #print(repr(o_view), file=sys.stderr)
input[0].close() input[0].close(force=True)
output[0].close() output[0].close(force=True)
info_input[0].close() info_input[0].close(force=True)
if unidentified is not None: if unidentified is not None:
unidentified_input[0].close() unidentified_input[0].close(force=True)
aligner.free() aligner.free()
logger("info", "Done.") logger("info", "Done.")