[Bioperl-l] fastq parsing problem
Chris Fields
cjfields at illinois.edu
Tue May 12 18:36:40 UTC 2009
On May 12, 2009, at 1:11 PM, Sendu Bala wrote:
> John Marshall wrote:
>> Michael Muratet wrote:
>>> I've got a problem parsing fastq output from the maq aligner. The
>>> parser is throwing an exception for the following record:
>>>
>>> @HWI-EAS146:3:1:2:177#0/1
>>> CTCCGCTNNCTTCTCAG[...]
>>> +
>>> @,AB=>-&&:5).;+*=[...]
>>>
>>> I looked up the line in fastq.pm that does the parsing:
>>>
>>> 116 my ($top,$sequence,$top2,$qualsequence) = [...]
>> This is the fastq parser from 1.5.2 or thereabouts, which had a bug
>> (the
>> $/ definition just above this code) that prevented it from parsing a
>> record with a quality line starting with "@". This was probably not
>> recognised as a bug for a long time due to the enduring myth that
>> fastq
>> quality lines always start with "!".
>
> I see you talked about it in the discussion page, but I think it
> might be time to change the wiki page as well:
> http://www.bioperl.org/wiki/FASTQ_sequence_format
>
> That caught me out as well. *sigh*
Updated, along with links to the MAQ FASTQ page and Wikipedia. I'll
update the module docs as well.
chris
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