Re: Converting fasta (with multiple sequences) into tabular using perl

[jwkrahn]

This appears to do what you require:

#!/usr/bin/perl
# fasta_to_tbl.pl
use strict;
use warnings;

die "Please specify suitable file\n" if @ARGV != 1;
my ( $fasta ) = @ARGV;

my $outfile = "$fasta.tbl";

open my $in,  '<', $fasta   or die "error reading $fasta. $!";
open my $out, '>', $outfile or die "error creating $outfile. $!";


while ( <$in> ) {
    if ( /^>/ ) {
        # Identifier!
        # "\t" TAB character for "tabular format"
        s/[:\s|,;].*/\t/s;
        print $out $_;
        next;
        }
    s/\s//g;
    if ( !/\w/ || eof $in ) {
        # empty line or end of file
        print $out "$_\n\n";
        }
    else {
        # Data
        print $out $_;
        }
    }

[rarenas]

Thank you! This is helpful!