ngsfilter clash if there is one (or two?) serie(s) of "n" longer than the primers
Clash of ngsfilter when a sequence record contains one or two series of "n" longer than the primers. I obtained the following message:
[RocheNoire:~/Desktop/co1_16s] pierretaberlet% ngsfilter -t ngs_co1_16s.txt --fasta -e 0 L002.obi.fasta > L002.obi.ngs.fasta L002.obi.fasta 2.8 % |#/ ] remain : 13:14:02 Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/bin/ngsfilter", line 451, in good,seq = annotate(seq,options) File "/Library/Frameworks/Python.framework/Versions/2.7/bin/ngsfilter", line 320, in annotate reversematch = [(p,p(sequence)) for p in primers if p is not None] File "/Library/Frameworks/Python.framework/Versions/2.7/bin/ngsfilter", line 148, in call tag=str(sequence[end:end+self.taglength].complement()) File "obitools/_obitools.pyx", line 553, in obitools._obitools.WrappedBioSequence.complement (src/obitools/_obitools.c:13753) File "obitools/_obitools.pyx", line 562, in obitools._obitools.WrappedBioSequence.complement (src/obitools/_obitools.c:13703) AttributeError
and the sequence record causing the crash was:
NS500639:5:H2WMCAFXX:2:11102:21949:20400_CONS ali_length=46; direction=left; seq_ab_match=29; score=13.2920129752; seq_a_mismatch=3; seq_b_deletion=0; seq_b_mismatch=10; seq_a_deletion=5; score_norm=0.288956803808; seq_b_insertion=1; seq_a_insertion=3; mode=alignment; seq_a_single=106; seq_b_single=103; agctggctgctgaacgccctcntaaggatattcgcgangnnnnnnnnnnnnnnnnnnnnnnaggtcttaaggnngannnnnnnnnnnnnnnnnnnnnnnnnnnnatgcaatcacgtaggcggcctaccgattcggcgtgtgatgaatgccaaggcgttgcgggactattttcgggatattggtcggatggttcttgctgccgagggtcgcaaggctaatgattcacacgccgactgctcgcagtatttttgtgtg