[Bioperl-l] Reading and writing fastq files

[Ben Bimber]

i think you want:

$outr->write_seq($seq);

instead of trying to write $in.

-ben



On Sun, Feb 6, 2011 at 2:42 PM, shalabh sharma
<shalabh.sharma7 at gmail.com> wrote:
> Hi,
>    i am trying to read and write fastq files.
> I can read them and can change format (like fastq files to fasta) but when i
> try to write them back as 'fastq' format i am getting a warning:
>
> --------------------- WARNING ---------------------
> MSG: You can't write FASTQ without supplying a Bio::Seq::Quality object!
>
> and i am not getting getting any output.
> I am using bioperl 1.61
>
> My part of code looks like this:
>
> #!/usr/bin/perl -w
> use Bio::SeqIO;
> $in = Bio::SeqIO->new(-file => "$ARGV[0]", -format => 'fastq');
> - - - - -- -
>  - - - -- - -
>
> while(my $seq = $in->next_seq){
>         -- - - - -  -
>         - - - - - - -
>         $outr->write_seq($in);
> }
>
> fastq file looks like this:
>
> @1477:2:1:1143:901/1
> NTCGGTACAGCGACAAACAGACGATATCACCGGCTAAGCTCGATGGTGGTTACGGATGCGAAACAACGTGGTAGCTCAGGTAAGGATTTAAGGCCTTCTATTACTTTGGTTAATGAAGGCCGTGAACCAATTTGTGTGCCTGGACTCAATA
> +
> BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
> @1477:2:1:1143:901/2
> ATTAACCACCGCACCTGCAGGCATTACATAATGCACCGCGATATTGGTTCCAGCCACCCAAATTGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNGCTTCCCATCGNTAACCACCATC
> +
> \cf_ff[fdcfebcad^e\YadcYdceWe\^deaed_Y[c\dd[ce^bfbdbRLWa]R^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
> @1477:2:1:1166:923/1
> NTACTCCAGCGGAAAATGCTACGCTTCGATCATTGCTAATATCAAATAACGTTTTTTGCTCAACCGATGAGCTTTCCAGTCGGTAAGGAAGCGGTTCATTAGCCTGAGCGAGCGGGTCAAAAACGATATCTTCGCGAGCTTCATACTTAAC
> +
> BKOHONNNMN_______________BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
>
> I would really appreciate if some one can help me out.
>
> Thanks
> Shalabh
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