[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 
	
	

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