build_fasta_hash.pl

#! /usr/bin/perl
use strict; use warnings;

# This script will parce a fasta file and create
# a hash where keys are fasta ids (everything after '>')
# and values are fasta sequences of arbitrary length (could be
# DNA, RNA, protein). I'm not checking the symbols in the sequence

my $fasta_file = shift or die "Please, provide a fasta file: $!\n";

open( my $fasta_fh, "<", $fasta_file) or die "Cannot open fasta file: $!\n";

my %id2seq;
my $id = ();

while ( my $line=<$fasta_fh> )
{
    chomp $line;
    if ( $line =~ m/^>(.+)/ )
    {
        $id = $1;
    }
    else
    {
       $id2seq{$id} .= $line 
    }
}