[Bioperl-l] create Bio::AlignIO object from hash
roy.chaudhuri at gmail.com
Wed Jan 13 07:52:58 EST 2010
Upload them to Bugzilla as patches, and one of the devs will review your
changes and incorporate them into bioperl-live:
On 11/01/2010 16:27, Adam Witney wrote:
> Ah excellent, thanks Roy. I was indeed thinking about it the wrong
> In the process of writing this i have created a
> Bio::Tools::Run::Phylo::Phylip::Pars class
> which is essentially just a modified copy of ProtPars. I have also
> fixed a few typos and possible bugs in
> Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm Bio/AlignIO/phylip.pm
> I am of course happy to send these back in to the project... how
> would i best do this?
> On 11 Jan 2010, at 13:54, Roy Chaudhuri wrote:
>> Actually, I guess some sample code would be more helpful:
>> use Bio::LocatableSeq; use Bio::SimpleAlign; use Bio::AlignIO; my
>> $seq1=Bio::LocatableSeq->new(-id=>'one', -seq=>'AT-CG', -start=>1,
>> -end=>4); my $seq2=Bio::LocatableSeq->new(-id=>'two',
>> -seq=>'A--CG', -start=>1, -end=>3); my
>> $seq3=Bio::LocatableSeq->new(-id=>'three', -seq=>'ATTCG',
>> -start=>1, -end=>5); my
>> Cheers, Roy.
>> On 11/01/2010 13:40, Roy Chaudhuri wrote:
>>> Hi Adam,
>>> I'm guessing you actually want to create a Bio::SimpleAlign
>>> object (representing an alignment), rather than a Bio::AlignIO
>>> object (which is just for reading/writing alignment files).
>>> Bio::SimpleAlign has a documented new method that allows you to
>>> construct an alignment from Bio::LocatableSeq objects, which are
>>> similar to Bio::Seq objects but include gaps and start/end
>>> coordinates to describe their relationship to other sequences in
>>> the alignment.
>>> On 11/01/2010 12:21, Adam Witney wrote:
>>>> I am writing a script to automate the running of Phylip Pars.
>>>> In the process i have to create a Bio::AlignIO object from a
>>>> set of data that i have in a hash.
>>>> I could write the hash data into a phylip file and then load
>>>> the Bio::AlignIO from that file, but i wondered if i could skip
>>>> the writing and then reading of a temporary file ?
>>>> thanks for any help
>>>> adam _______________________________________________ Bioperl-l
>>>> mailing list Bioperl-l at lists.open-bio.org
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