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problem runnig obigrep
#1
I'm trying to run obigrep but I got this error message.


obigrep -p 'score_norm>3.8 and score>40' paired.fastq > paired.good.fasta
paired.fastq   0.1 % |/                                                  ] remain : 00:00:13Traceback (most recent call last):
  File "/usr/local/bin/obigrep", line 42, in <module>
    for seq in goodSeq(entries):
  File "src/obitools/options/_bioseqfilter.pyx", line 79, in sequenceFilterIterator (build/temp.linux-x86_64-2.7/pyrex/obitools/options/_bioseqfilter.c:3970)
  File "src/obitools/options/_bioseqfilter.pyx", line 52, in obitools.options._bioseqfilter.filterGenerator.sequenceFilter (build/temp.linux-x86_64-2.7/pyrex/obitools/options/_bioseqfilter.c:3153)
  File "src/obitools/options/_bioseqfilter.pyx", line 53, in genexpr (build/temp.linux-x86_64-2.7/pyrex/obitools/options/_bioseqfilter.c:2446)
  File "<string>", line 1, in <module>
NameError: name 'score_norm' is not defined
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#2
Some of your sequences have no score_norm attribute. Add the following condition on the command should solve the problem :

obigrep -A score_norm -A score -p 'score_norm>3.8 and score>40' paired.fastq > paired.good.fasta

All the best
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#3
Thak you it works

But now I have a problem with the ngs filter command :

ngsfilter -u nosample.fasta -t nosample.ngsfilter paired.good.fasta


Traceback (most recent call last):
  File "/usr/local/bin/ngsfilter", line 426, in <module>
    primers=readTagfile(options.taglist)
  File "/usr/local/bin/ngsfilter", line 199, in readTagfile
    len(p['tags'][0]) if p['tags'][0]!='-' else None,
TypeError: 'NoneType' object has no attribute '__getitem__'




Here is my nosample.ngsfilter file :

experience FTF015_100um_R1 -:- GGWACWGGWTGAACWGTWTAYCCYCC GTAAACTTCAGGGTGACCAAARAAYCA F



can you identify the problem ??

thanks
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