[Cogs-guts] AESIG graph_to_seq.pl,NONE,1.1

[kirovs <ki...@us...>]

Update of /cvsroot/cogs/AESIG
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv18247

Added Files:
	graph_to_seq.pl 
Log Message:
visualize sequences for a graph

--- NEW FILE: graph_to_seq.pl ---
use Bio::SeqIO;
my $sf=shift;
my $gf=shift;
my $win=shift;
open (GF,$gf)||die;
my $seqio=new Bio::SeqIO(-file=>$sf,-format=>'fasta');
my %seqs;
while (my $seq=$seqio->next_seq) {
        $seqs{$seq->id}=$seq;
	my $ps=$seq->translate;
	$pss{$seq->id}=$ps;
}
my $head=<GF>;
while (my $buf=<GF>) {
	chomp $buf;
	my ($s1,$s2,$v)=split(/[\s\t]/,$buf);
	my ($id1,$p1)=split(/_/,$s1);
	$p1++;
	my ($id2,$p2)=split(/_/,$s2);
	$p2++;
	my $c1=int($p1/3);
	my $cm1=$p1%3;
	my $c11=$c1+3;
	$c1++ if ($c1==0);
	my $codon1=$pss{$id1}->subseq($c1,$c11);
	
 my ($id2,$p2)=split(/_/,$s2);
        my $c2=int($p2/3);
        my $cm2=$p2%3;
	my $c21=$c2+3;
	$c2++ if ($c2==0);
        my $codon2=$pss{$id2}->subseq($c2,$c21);
	my $sseq1=$seqs{$id1}->trunc($p1,$p1+$win-1);
	my $psseq1=$sseq1->translate;
	
	print $psseq1->seq,' ',$seqs{$id1}->subseq($p1,$p1+$win-1)," $p1 ";
	print "$codon1 $cm1\t\t";
	
	my $sseq2=$seqs{$id2}->trunc($p2,$p2+$win-1);
	my $psseq2=$sseq2->translate;
	print $psseq2->seq,' ',$seqs{$id2}->subseq($p2,$p2+$win-1)," $p2",$v;
	print " $codon2 $cm2\n";

}