[Bioperl-l] Fastq - is it flush, or not?

[Nestor Zaburannyi]

Chris,

cat myfile.fastq | grep -v ^@ | grep -v ^+$ | awk '{ print $0 " = " length($0) }' | grep -v 50

gives empty string and that means every sequence AND every quality string has exactly 50 characters. So, no clipping present, that's for sure. Any other ideas anyone?

Sincerely yours
Nestor



Monday, July 11, 2011, 2:17:07 PM, you wrote:

> The error appears to be in revcom(), so my guess is something with clipping of the quality data?  Hard so say for sure, though, w/o seeing the data and testing it.  

> chris

> On Jul 11, 2011, at 3:47 AM, Nestor Zaburannyi wrote:

>> Dear All.

>> I need to reverse-complement a huge *.fastq file. I try to

>> while (my $seq = $in->next_seq)
>>    {
>>    $out->write_seq($seq->revcom);
>>    }

>> However, it stops with:

>> ------------- EXCEPTION -------------
>> MSG: Can not get a reverse complement. The object is not flush.
>> STACK Bio::Seq::Meta::Array::revcom /usr/share/perl5/Bio/Seq/Meta/Array.pm:648


>> Adding

>> $seq->force_flush('1');

>> helps, but is it necessary and proper way? Sequences seem to be "flush".

>> Sincerely yours
>> Nestor

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-- 
З повагою,
 Nestor                            mailto:nestor at linuxmail.org