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|
#!/usr/bin/perl
use strict;
my $d = $ARGV[0];
my $fastaFile = $ARGV[1];
my $listFile = $ARGV[2];
my @ids = ();
my @seqs = ();
my @weights = ();
my @cWeights = ();
my %hashID = {};
open(FILE, $fastaFile) or die "Can't open $fastaFile\n";
my $count = 0;
while(my $line = <FILE>){
if($line =~ />(.*)/){
my $name = $1;
$ids[$count] = $name;
$ids[$count] =~ /^.*_\d+_(\d+)/;
#print "$1\n";
$weights[$count] = $1;
$hashID{$name} = $count;
$count++;
}
else{
chomp($line);
if($seqs[$count - 1] ne undef){
$seqs[$count - 1] = $seqs[$count - 1] . $line;
}
else{
$seqs[$count - 1] = $line;
}
}
}
close(FILE);
#for(my $i = 0; $i < $count; $i++){
# print "$i $ids[$i] $weights[$i]\n";
#}
my @consensus = ();
open(FILE, $listFile) or die "Can't open $listFile\n";
while(my $line = <FILE>){
my @tokens = split(/ /,$line);
my $dLocal = shift(@tokens);
my $N = shift(@tokens);
if($d == $dLocal){
for(my $i = 0; $i < $N; $i++){
my $clust = shift(@tokens);
my @cluster = split(/,/,$clust);
my $cSize = scalar(@cluster);
my $otuWeight = $weights[$hashID{$cluster[0]}];
my $bestWeight = $weights[$hashID{$cluster[0]}];
my $bestJ = $hashID{$cluster[0]};
for(my $j = 1; $j < $cSize; $j++){
if($weights[$hashID{$cluster[$j]}] > $bestWeight){
$bestJ = $hashID{$cluster[$j]};
$bestWeight = $weights[$hashID{$cluster[$j]}];
}
$otuWeight += $weights[$hashID{$cluster[$j]}];
}
$consensus[$i] = $seqs[$bestJ];
$cWeights[$i] = $otuWeight;
#print "$i $consensus[$i]\n";
}
for(my $i = 0; $i < $N; $i++){
print ">C${i}\n";
print "$consensus[$i]\n";
}
}
}
close(FILE);
|
