[Bioperl-l] warning: Bio::Index::Fastq;

[Smithies, Russell]

To cover the possibility of multiple '@' symbols (apparently there is no single word to describe this symbol) shouldn't it be:

if (/^@+[A-Z]/) {

or

if (/^@[@A-Z]+/) {


--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Fields, Christopher J
Sent: Wednesday, 12 March 2014 8:20 a.m.
To: Ehsan Habibi
Cc: BioPerl List; Peter Cock
Subject: Re: [Bioperl-l] warning: Bio::Index::Fastq;

Wouldn't this fail with a qual string like '@DDDDDFFFFFIIIDCBBBB'?  Preferentially it should cover the FASTQ torture test suite that Peter set up (which IIRC has a few like this).

chris

On Mar 11, 2014, at 1:33 PM, Ehsan Habibi <eh_mcb at yahoo.com> wrote:

> I changed the following part of the code (Bio/Index/Fastq.pm) and now it works perfect :)
>      # Main indexing loop
> while (<$FASTQ>) {
>  if (/^@[A-Z]/) {
> 
> 
> 
> 
> 
> On Tuesday, March 11, 2014 5:40 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> On Mar 11, 2014, at 11:16 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 
> 
> > On Tue, Mar 11, 2014 at 4:01 PM, EpiMAN <eh_mcb at yahoo.com> wrote:
> >> test <http://bioperl.996286.n3.nabble.com/file/n17374/test>
> >> 
> >> grep -C 10 "^@@DDDDDFFFFFIIIDCBBBB"
> > 
> > Very helpful - it does look like it came from a valid FASTQ (the -- 
> > lines are where grep cuts each snippet).
> > 
> > I think I can explain this, see:
> > https://github.com/bioperl/bioperl-live/commit/b45e2d33984cf283b846d
> > 7c146ec9e0e9ebae67f
> > 
> > Chris' hack handled quality lines starting with a single '@'
> > sign, but multiple '@' signs like your examples which start '@@' 
> > instead.
> > 
> > Peter
> 
> 
> We probably need a stricter index method analogous to the Bio::SeqIO::fastq parser.  I'll see if I can eek out time today to look into it.
> 
> chris
> 
> 
> 


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