[Bio BB] Convert PFAM to FASTA
Cook, Malcolm
MEC at Stowers-Institute.org
Wed May 31 12:31:59 EDT 2006
If you happen to have perl and bioperl installed, you can convert
myfile.pfam to myfile.pfam.fa with the following unix one-liner:
cat myfile.pfam | perl -MBio::AlignIO -e 'select
Bio::AlignIO->newFh(-format => "fasta"); $in =
Bio::AlignIO->newFh(-format => "pfam", -fh => \*STDIN); print while
<$in>' > myfile.pfam.fa
________________________________
From:
bio_bulletin_board-bounces+mec=stowers-institute.org at bioinformatics.org
[mailto:bio_bulletin_board-bounces+mec=stowers-institute.org at bioinformat
ics.org] On Behalf Of Iain Wallace
Sent: Wednesday, May 31, 2006 5:34 AM
To: bio_bulletin_board at bioinformatics.org
Subject: [Bio BB] Convert PFAM to FASTA
Hi all,
Does anyone know of a programme that can take a pfam alignment
and convert it into fasta?
Thanks
Iain
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/bbb/attachments/20060531/dc9aeec1/attachment.html>
More information about the BBB
mailing list