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#!/usr/bin/env perl
use strict;
use warnings;
use lib ($ENV{EUK_MODULES});
use Fasta_reader;
my $usage = "usage: $0 targets.fasta\n\n";
my $target_fasta_file = $ARGV[0] or die $usage;
main: {
my $fasta_reader = new Fasta_reader($target_fasta_file);
my %seqs = $fasta_reader->retrieve_all_seqs_hash();
foreach my $acc (keys %seqs) {
my $sequence = $seqs{$acc};
my $seq_len = length($sequence);
if ($seq_len < 500) { next; }
my $bubble_missing_seq = $sequence;
$bubble_missing_seq = substr($bubble_missing_seq, 0, 200) . substr($bubble_missing_seq, 350);
my $new_gene_acc = $acc;
$new_gene_acc =~ s/\W/_/g;
print ">isoA-$new_gene_acc;$new_gene_acc\n$sequence\n"
. ">isoB-$new_gene_acc;$new_gene_acc\n$bubble_missing_seq\n";
}
exit(0);
}
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