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problem runnig ngs filter
#1
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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#2
I'm also having trouble with ngsfilter. I tried using the wolf tutorial files and ngsfilter works fine, however it does not work when I use my own files.

Input for the wolf files:
> ngsfilter -t wolf_diet_ngsfilter.txt -u wolf.bad.fastq wolf_P.good.fastq > wolf_P.samples.fastq
Started working no problem and produced sensible output files

Input for my files:
> ngsfilter -t fox_ngsfilter.txt -u fox.bad.fastq AJM201603.fastq > fox.good.fastq

Output for my files:
Traceback (most recent call last):
 File "/teampoo/obitools/OBITools-1.1.22/export/bin/ngsfilter", line 426, in <module>
   primers=readTagfile(options.taglist)
 File "/teampoo/obitools/OBITools-1.1.22/export/bin/ngsfilter", line 214, in readTagfile
   cf=forward.complement()
 File "/teampoo/obitools/OBITools-1.1.22/export/bin/ngsfilter", line 121, in complement
   p.align.seqB=p.sequence
 File "src/obitools/align/_dynamic.pyx", line 249, in obitools.align._dynamic.DynamicProgramming.seqB.__set__ (build/temp.linux-x86_64-2.7/pyrex/obitools/align/_dynamic.c:3568)
 File "src/obitools/align/_dynamic.pyx", line 88, in obitools.align._dynamic.allocateSequence (build/temp.linux-x86_64-2.7/pyrex/obitools/align/_dynamic.c:1659)
 File "src/obitools/_obitools.pyx", line 259, in obitools._obitools.BioSequence.__str__ (build/temp.linux-x86_64-2.7/pyrex/obitools/_obitools.c:5625)
 File "src/obitools/_obitools.pyx", line 696, in obitools._obitools.DNAComplementSequence.getStr (build/temp.linux-x86_64-2.7/pyrex/obitools/_obitools.c:17603)
 File "src/obitools/_obitools.pyx", line 699, in genexpr (build/temp.linux-x86_64-2.7/pyrex/obitools/_obitools.c:17784)
 File "src/obitools/_obitools.pyx", line 705, in obitools._obitools.DNAComplementSequence.getSymbolAt (build/temp.linux-x86_64-2.7/pyrex/obitools/_obitools.c:18156)
KeyError: '0'

I cannot see any obvious differences between my ngsfilter text file and the wolf one, except that mine includes tags at both ends of the construct.

wolf_diet    13a_F730603      aattaac  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F       @
wolf_diet    15a_F730814      gaagtag  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F       @
wolf_diet    26a_F040644      gaatatc  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F       @
wolf_diet    29a_F260619      gcctcct  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F       @

fox_scat_12SV5 702a ggagctt:agcgaag TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @
fox_scat_12SV5 702b ggagctt:agctctc TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @
fox_scat_12SV5 702c ggagctt:ggagctt TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @
fox_scat_12SV5 918a gccacat:agaggat TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @
fox_scat_12SV5 918b gccacat:agatgca TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @
fox_scat_12SV5 918c gccacat:gccacat TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @

My input fastq file is as it came direct from the sequencer, so I doubt there will be any formatting error there.

Can anyone help???

Thanks!
Anna
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#3
An update from me - I've fixed this problem now with the help of a colleague, and once we found the problem it was an easy fix. Just in case it helps others: somehow gremlins got into my ngsfilter text file and inserted a space into the middle of about 10 of the 300+ sample names. This meant that the second part of each sample name was misinterpreted as a very strange primer sequence, producing errors. Finally figured this out using the --DEBUG option within the ngsfilter command.
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