[Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq

Roy Chaudhuri roy.chaudhuri at gmail.com
Tue Jul 27 10:16:27 EDT 2010


Hi Alan,

Another case for the deobfuscator:
http://bioperl.org/cgi-bin/deob_interface.cgi

A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say 
$seqqual->seq to get the sequence as a string.

Cheers.
Roy.

On 27/07/2010 15:10, Alan Twaddle wrote:
> Hello,
>
>       I am curious as to how I am supposed to use SeqIO::fastq to read
> in a fastq file and then obtain the nucleotide sequence from that. I
> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't
> seen a method within that module that returns the nucleotide sequence.
> Please, let me know if you have any suggestions!
>
> Thank you very much!!
>



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