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#!/usr/bin/env perl
use strict;
use warnings;
use lib($ENV{EUK_MODULES});
use Fasta_reader;
my $usage = "\n\n\tusage: $0 trin_before.fa trin_after.fa\n\n";
my $trin_before_file = $ARGV[0] or die $usage;
my $trin_after_file = $ARGV[1] or die $usage;
main: {
my %trin_seqs_before = &parse_trin_fa($trin_before_file);
my %trin_seqs_after = &parse_trin_fa($trin_after_file);
foreach my $acc (keys %trin_seqs_after) {
my $seq_before = $trin_seqs_before{$acc} or die "Error, no before transcript for [$acc]";
my $seq_after = $trin_seqs_after{$acc} or die "Error, no after transcript for [$acc]";
if ($seq_before eq $seq_after) {
print "* $acc identical\n";
}
else {
my $filename = $acc;
$filename =~ s/\W/_/g;
open(my $ofh, ">$filename") or die $!;
print $ofh ">before\n$seq_before\n"
. ">after\n$seq_after\n";
close $ofh;
my $ret = system("clustalw2 $filename");
if ($ret) {
die $!;
}
}
}
exit(0);
}
####
sub parse_trin_fa {
my ($file) = @_;
my $fasta_reader = new Fasta_reader($file);
my %seqs = $fasta_reader->retrieve_all_seqs_hash();
return(%seqs);
}
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