Perl script to read multi fasta sequence one by one

Jit — Fri, 06 Apr 2018 09:01:17 -0500

#!/usr/bin/env perl

use strict;
use warnings;

#USAGE
#perl rohanRun.pl seq.fa
my $outfile='tmp.fa';
my $fastaSeq_ref = readfasta ("$ARGV[0]");
my %fastaSeq = %$fastaSeq_ref;
foreach my $key ( keys %fastaSeq) {
open (OUT, ">$outfile") or die "couldn't open the file $outfile $!";
print OUT "$key\n$fastaSeq{$key}\n";

}


sub readfasta 
{
  (my $file)=@_;
	my %sequence;
	my $header;
	my $temp_seq;
	
	#suppose fasta files contains multiple sequences;
	 
	open (IN, "<$file") or die "couldn't open the file $file $!";
	
	while ()
	{	
		chop;
		next if /^\s*$/; #skip empty line 
		if ($_ =~ /^>/)  #when see head line
		{	
			$header= $_;
			if ($sequence{$header}){print colored("#CAUTION: SAME FASTA HAS BEEN READ MULTIPLE TIMES.\n#CAUTION: PLEASE CHECK FASTA SEQUENCE:$header\n","red")};
			if ($temp_seq) {$temp_seq=""} # If there is alreay sequence in temp_seq, empty the sequence file
			
		}
		else # when see the sequence line 
		{
		   s/\s+//g;
		   $temp_seq .= $_;
		   $sequence{$header}=$temp_seq; #update the contents
		}
	
	}
	
	return \%sequence;
}

BOL: Perl script to read multi fasta sequence one by one

Perl script to read multi fasta sequence one by one