[Bioperl-l] seqIO.pm

Fields, Christopher J cjfields at illinois.edu
Mon Nov 21 11:57:29 EST 2011

On Nov 21, 2011, at 10:15 AM, Peter Cock wrote:

> On Thu, Nov 17, 2011 at 1:07 AM, Nathan Taylor <zntayl at gmail.com> wrote:
>> Hello,
>>   Can SeqIO.pm convert a file of fastq reads into .phd files. Or,
>> barring that, a file of fastas and file of quals into .phd files?
>> Many thanks,
>> Nathan
> In principle that is possible (e.g. Biopython can do fastq to phd).
> Have you tried using BioPerl's SeqIO to do this? Was there an
> error message?
> Peter

This should be possible in either circumstance (FASTQ should be more straightforward), there is a Bio::SeqIO::phd for this purpose.  Nathan, if you run into problems with that conversion let us know.


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