[Bioperl-l] create Bio::AlignIO object from hash

[Roy Chaudhuri]

Upload them to Bugzilla as patches, and one of the devs will review your 
changes and incorporate them into bioperl-live:
http://www.bioperl.org/wiki/HOWTO:SubmitPatch

Roy.

On 11/01/2010 16:27, Adam Witney wrote:
>
> Ah excellent, thanks Roy. I was indeed thinking about it the wrong
> way.
>
> 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/Base.pm
> Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm Bio/AlignIO/phylip.pm
> Bio/Tools/Run/Alignment/Clustalw.pm
>
> I am of course happy to send these back in to the project... how
> would i best do this?
>
> Cheers
>
> adam
>
>
> 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
>> $aln=Bio::SimpleAlign->new(-seqs=>[$seq1,$seq2,$seq3]);
>> Bio::AlignIO->new(-format=>'phylip')->write_aln($aln);
>>
>> 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.
>>>
>>> Roy.
>>>
>>> On 11/01/2010 12:21, Adam Witney wrote:
>>>> Hi,
>>>>
>>>> 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
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>