Parse sorghum genome.pl

#! /usr/bin/perl -w
# *************************************************************
# This Programme does the following in sequence
# -> Parses a multi fasta
# -> Write each sequence as individual files
# Author : Rajkumar (r@rajkumar.in)
# Release: AUG 2010
# *************************************************************
 
# Libraries
	use strict;
	use Bio::Perl;
	use Bio::SearchIO;
	use Parallel::ForkManager;

# Variables
	my $path       = "/home/raj/bio/user/rk/genome";
	my $multifasta = "$path/sb_genome.fa";
	my $resdir     = "$path/individual_files_fasta";
	my $zipdir     = "$path/individual_files_zip";
	my ($i,$file)  = $_;
	my (@files)    = @_;

# At the top: Time Start
	my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);

# Multi-threading
	my $midstop     = "0"; # If midstop is 0 it deals with all the files		
	my $pm          = new Parallel::ForkManager(8);

 
# Getting the grip of files
 	if (-e "$resdir") {`rm  -fr $resdir`;} if (! -e "$resdir") {`mkdir $resdir`;}
 	if (-e "$zipdir") {`rm  -fr $zipdir`;} if (! -e "$zipdir") {`mkdir $zipdir`;}
 
# Let's Hack
	

	# count the fasta
	my $c_fasta = `grep -c ">" $multifasta`; chomp $c_fasta;

	my $in  = Bio::SeqIO->new(-file => "$multifasta", -format => 'Fasta');
	my ($identifier, $sequence) = $_;
 	
	$i = 0;
	while ( my $seq = $in->next_seq() ) {
		$identifier = $seq->id;
  		$sequence = $seq->seq;
 		$i++;

		$pm->start and next;
		

		my $percent = ($i/$c_fasta)*100;
		$percent = sprintf("%.2f", $percent);

		
		my $count_seq = length($sequence);
		$count_seq = $count_seq/1000000;
		$count_seq = sprintf("%.2f", $count_seq);

		my $fasta = ">".$identifier."_Size:".$count_seq."Mb\n".$sequence."\n";
		my $id_size = $identifier."_Size:".$count_seq."Mb.fa";
 
		print "\n\tInitiated [$i of $c_fasta] | $percent% ";

		open (FH, ">".$resdir."/".$id_size);
		print FH $fasta ;
		close FH ;
		

		chdir $resdir;		
		`zip $zipdir/$id_size.zip $id_size`;
		
 		$pm->finish;
	}

	$pm->wait_all_children;

	`rm -fr $resdir`;
	
	print "\nAll Done!\n\n";
 
 
# At the End: Time Calculation
	my ($sec_,$min_,$hour_,$mday_,$mon_,$year_,$wday_,$yday_,$isdst_) = localtime(time);
	my $days = $mday_-$mday;
	my $hours = $hour_-$hour;
	my $mins = $min_-$min;
	my $secs = $sec_-$sec;
	print "\n------------------------\nDuration: ";
	if ($days>0) { print "$days days";}
	if ($hours>0) { print ": $hours hours";}
	if ($mins>0) { print ": $mins mins";}
	if ($secs>0) { print ": $secs secs";}
	print "\n------------------------\n";
 
# END