Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
diff phyloconversion/uniprotfasta2phytab.pl @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloconversion/uniprotfasta2phytab.pl Tue Mar 11 12:19:13 2014 -0700 @@ -0,0 +1,38 @@ +#!/usr/bin/perl -w + +use strict; + +use FindBin; +use lib "$FindBin::Bin/lib"; +use Bio::DB::Fasta; +use Bio::SeqIO; +use Bio::Seq; + +#inputs +my $infile=shift(@ARGV); +my $partition=shift(@ARGV); +#my $delpipes=shift(@ARGV); +my $species; + +my $seqid; +# open infile fasta file +my $in_obj = Bio::SeqIO->new(-file => $infile, '-format' =>'fasta'); + +while (my $seq = $in_obj->next_seq() ) { + my $sequence = $seq->seq; + my @rawid = split(/\|/, $seq->id); + $seqid = $rawid[1]; +# $seqid = $seq->id; + + $sequence =~ s/\n//g; + $species = $seq->desc; + #species Name is after OS= + $species =~ s/.+OS\=//; + $species =~ s/.+OS\=//; + #species Name is before GN= sometimes PE= + $species =~ s/ GN\=.+//; + $species =~ s/ PE\=.+//; + $species =~ s/ /_/g; + + print $species."\t".$partition."\t".$seqid."\t".$sequence."\n"; +}