[Biopython] Bio.AlignIO and Bio.SearchIO

[Michiel de Hoon]

Hi Peter,
Thanks for your reply. Yes I have a fully aligned sequence in the FASTA file, with dashes showing the indels.
Best,-Michiel
 

    On Wednesday, May 24, 2017 6:22 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
 

 Hi Michiel,

Both use SeqRecord objects internally, so it ought to be possible.
Presumably you would assume the query and match coordinates
were for the full aligned sequence in the FASTA file?

Peter

On Fri, May 19, 2017 at 9:41 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Dear all,
>
> Is there some easy way to convert a Bio.Align.MultipleSeqAlignment object
> into a Bio.SearchIO.QueryResult ?
> The reason I'm asking is that I am trying to convert a pairwise sequence
> alignment in Fasta format into PSL format.
> I am hoping to read the Fasta file with Bio.AlignIO, then convert the
> Bio.Align.MultipleSeqAlignment object into a Bio.SearchIO.QueryResult
> object, and write it out as PSL using Bio.SearchIO.
>
> Thanks,
>
> -Michiel
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython


   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20170524/a212c2ec/attachment.html>