[Biopython] Concatenate to aligned sequences

[Vincent Davis]

Thanks
Vincent

Vincent Davis
720-301-3003


On Thu, Feb 14, 2013 at 10:29 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Thu, Feb 14, 2013 at 5:20 PM, Vincent Davis <vincent at vincentdavis.net>
> wrote:
> > I have 2 fasta files from a mucle alignment. Both have the same number of
> > sequences from the same organism. If I what to concatenate the pairs of
> > sequences what it the  best way to do this.
> > Right now I am doing this:
> >
> > def concatenate(fa1, fa2):
> >     fa1open = open(fa1, "rU")
> >     fa2open = open(fa1, "rU")
> >     fa1dict =  SeqIO.to_dict(SeqIO.parse(fa1open, "fasta"))
> >     fa2dict =  SeqIO.to_dict(SeqIO.parse(fa2open, "fasta"))
> >     fa1open.close()
> >     fa2open.close()
> >     # check that both files have the same sequnce id's
> >     if set(fa1dict.keys()) != set(fa2dict.keys()):
> >         print(fa1dict.keys(), fa2dict.keys())
> >         print('The fasta files do not have the same sequences')
> >     bothdict = {}
> >     bothlist = []
> >     count = 1
> >     for key in fa2dict.keys():
> >         bothdict[key] = fa2dict[key]
> >         bothdict[key].seq = fa2dict[key].seq + fa1dict[key].seq
> >         bothlist.append(bothdict[key])
> >     return bothdict, bothlist
> >
> > Vincent Davis
> > 720-301-3003
>
> Have you tried loading the two alignment files via AlignIO,
> sorting by name if required, and adding the alignment objects?
>
>
> http://biopython.org/DIST/docs/api/Bio.Align.MultipleSeqAlignment-class.html#__add__
>
> Peter
>