[Bioperl-l] randomizing fastq sequences

[Frank Schwach]

If memory is an issue then I guess you could create a file of just the 
sequence IDs (one per line), then shuffle those (using List::Util like 
Simon demonstrated). In the end you would substitute the IDs for the 
whole fastq entry again, which you can do without reading an entire file 
into memory (might be bit slow but that probably doesn't
matter)
Frank


simon andrews (BI) wrote:
> On 7 Feb 2011, at 22:07, shalu sharma wrote:
>
>   
>> Hi,
>>   i am trying to test one program for which i need to change order of
>> sequences in a fastq file.
>> My fastq file contains about 50,000 sequences.
>> Is there any script that can do this task?
>>     
>
> Since FastQ is supported in SeqIO you could do something like (untested):
>
> #!/usr/bin/perl
> use warnings;
> use strict;
> use List::Util 'shuffle';
> use Bio::SeqIO;
>
> my @seqs;
>
> my $in = Bio::SeqIO->new(-file => 'your_intput.fastq',
> 			 -format => 'Fastq');
>
> while (my $seq = $in -> next_seq()) {
>     push @seqs,$seq;
> }
>
> @seqs = shuffle(@seqs);
>
> my $out = Bio::SeqIO->new(-file => '>your_output.fastq',
> 			  -format => 'Fastq');
>
> foreach my $seq (@seqs) {
>     $out->write_seq($seq);
> }
>
> ## End
>
> This has the disadvantage that it will hold all of the sequences in memory whilst shuffling, but I don't think there's an easy way around that.
>
> Simon.
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