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#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fasta_reader;
my $usage = "usage: $0 [multiFastaFile] [NO_FULL_HEADER_FLAG=0]\n\n";
my $input = $ARGV[0] || *STDIN{IO};
my $NO_FULL_HEADER_FLAG = $ARGV[1] || 0;
unless (-f $input || ref $input eq 'IO::Handle') {
die "Error, input not established.";
}
main: {
my $fasta_reader = new Fasta_reader($input);
while (my $seq_obj = $fasta_reader->next()) {
my $sequence = $seq_obj->get_sequence();
my $header = $seq_obj->get_header();
if ($NO_FULL_HEADER_FLAG) {
$header = $seq_obj->get_accession();
}
print "$header\t$sequence\n";
}
exit(0);
}
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