BOL: Calculate ATGC percentage in parallel with perl

BioScripts
Jit
Calculate ATGC percentage in parallel with perl

Calculate ATGC percentage in parallel with perl

By Jit 2861 days ago

#!/usr/bin/perl

use strict;
use Parallel::ForkManager;
use Bio::SeqIO;

#usage: perl testParallel.pl <multi fasta infile>

my %sequences;
my $seqio = Bio::SeqIO->new(-file => "$ARGV[0]", -format => "fasta");
while(my$seqobj = $seqio->next_seq) {
    my $id  = $seqobj->display_id;    # there's your key
    my $seq = $seqobj->seq;           # and there's your value
    $sequences{$id} = $seq;
}

  my $max_procs = 5;
  my @names = keys %sequences;

  # hash to resolve PID's back to child specific information
  my $pm =  new Parallel::ForkManager($max_procs);

 # Setup a callback for when a child finishes up so we can
  # get it's exit code
  $pm->run_on_finish (
    sub { my ($pid, $exit_code, $ident) = @_;
      #print "** $ident just got out of the pool ".
        "with PID $pid and exit code: $exit_code\n";
    }
  );

  $pm->run_on_start(
    sub { my ($pid,$ident)=@_;
     #print "** $ident started, pid: $pid\n";
    }
  );

  $pm->run_on_wait(
    sub {
      #print "** Have to wait for one children ...\n"
    },
    0.5
  );

  NAMES:
  foreach my $child ( 0 .. $#names ) {
    my $pid = $pm->start($names[$child]) and next NAMES;
    checkATCG($names[$child]);
    $pm->finish($child); # pass an exit code to finish
  }

  print "Waiting for Children...\n";
  $pm->wait_all_children;
  print "Everybody is out of the pool!\n";


sub checkATCG {
my $name=shift;
my $DNA=$sequences{$name};
my $length=length $DNA;
my $a=($DNA=~tr/A//);
my $b=($DNA=~tr/C//);
my $c=($DNA=~tr/G//);
my $d=($DNA=~tr/T//);
my $Total=$a+$b+$c+$d;
my $GC=($DNA=~s/GC/GC/g);
my $AT=($DNA=~s/AT/AT/g);
my $GCper=($GC/($Total)*100);
print"$name\t$Total\t$AT\t$GC\t$GCper:\n";

}

BOL

Jit

Our Sponsors

Calculate ATGC percentage in parallel with perl