Fetching Fasta

• Fetching Fasta as separate components

#!/usr/bin/perl -w

#----------------------------
# Description
# Remmoves the new line if exists in multifasta ignoring the sequence identifier
# Usage: Type infilename and Capture the output
#--------------------------------

# Use of functions
	use strict;
	use Bio::SeqIO;

# Variables
	my $argcount = @ARGV;
	if ($argcount !=1 ) {die "\n\t ->Usage: Type infile!\n\n";}
	my ($infile,$outfile) = @ARGV;
	my @seq;

# Function
	chomp($infile);
	my $input = `cat $infile`;
	
	$input =~ s/[\"|(|)|:]//g;
	$input =~ s/Note //g;
	$input =~ s/[ ]+/_/g;

	open(TEMP, ">tempfile");
	print TEMP $input;
	close TEMP;

	my $in  = Bio::SeqIO->new(-file => "tempfile", -format => 'Fasta');
	my $identifier;
	my $sequence;

	while ( my $seq = $in->next_seq() ) {
		$identifier = $seq->id;
  		$sequence = $seq->seq;

		print ">$identifier\n$sequence\n";
	}
	`rm tempfile`;
#END