ordinalHeaders.pl

#!/usr/bin/env perl
# Rewrite FASTA headers to increasing ordinals: S1, S2, S3..
#
# Samuel S. Shepard (vfn4@cdc.gov)
# 2015, Centers for Disease Control & Prevention

use Getopt::Long;
GetOptions(
            'keep-annotation|A'          => \$keepAnnot,
            'annot-with-header|H'        => \$headerAnnot,
            'name-annotation-format|N=s' => \$nameAnnotation,
            'only-name-format|O=s'       => \$onlyName,
            'pipe-format|P'              => \$pipeFormat
);
open( IN, '<', $ARGV[0] ) or die("$0 ERROR: Cannot open $ARGV[0].\n");

if ( scalar(@ARGV) != 1 ) {
    die("Usage:\n\tperl $0 <input.fasta> [-A] [-H] [-N <STR>] [-O <STR>]\n");
}

# PROCESS fasta data
$/ = ">";
$i = 0;
while ( $record = <IN> ) {
    chomp($record);
    @lines     = split( /\r\n|\n|\r/, $record );
    $oldHeader = shift(@lines);
    $ordinal   = 'S' . ( $i++ );
    $sequence  = join( '', @lines );

    if ($keepAnnot) {
        if ( $oldHeader =~ /{(.+)}/ ) {
            $ordinal .= "{$1}";
        }
    } elsif ($headerAnnot) {
        $ordinal .= "{$oldHeader}";
    } elsif ($nameAnnotation) {
        $ordinal = $nameAnnotation . '{' . $ordinal . '}';
    } elsif ($onlyName) {
        $ordinal = $onlyName;
    } elsif ($pipeFormat) {
        $ordinal .= '|' . $oldHeader;
    }

    if ( length($sequence) == 0 ) {
        next;
    } else {
        print '>', $ordinal, "\n";
        print $sequence, "\n";
    }
}
close(IN);
####################