davetang

#!/usr/bin/env perl
#
# Script that compares two files of IDs, that are on separate lines
# See http://stackoverflow.com/questions/2933347/comparing-two-arrays-using-perl
#

use strict;
use warnings;
use Array::Utils qw(:all);

davetang

#!/usr/bin/env perl

use strict;
use warnings;

my $usage = "Usage: $0 <infile.fa> <number> <length>\n";
my $fasta = shift or die $usage;
my $num = shift or die $usage;
my $len = shift or die $usage;

davetang

#!/usr/bin/env perl

use strict;
use warnings;

my $usage = "Usage: $0 <bp> <seed>\n";
my $num = shift or die $usage;
my $seed = shift or die $usage;

#set seed for reproducibility

davetang

#!/usr/bin/env perl
 
use strict;
use warnings;
 
my $data   = [];
my $t_data = [];
 
while(<>){
   chomp;

davetang

#!/usr/bin/perl

use warnings;
use strict;

my $BAILOUT=16;
my $MAX_ITERATIONS=1000;

my $begin = time();

davetang

#!/bin/env perl

use strict;
use warnings;

my $usage = "Usage: $0 <bam_flag>\n";
my $flag = shift or die $usage;

die "Please enter a numerical value\n" if $flag =~ /\D+/;

davetang

#!/bin/env perl

use strict;
use warnings;

#hash for filehandles
my %fh = ();

#read from stream
while (<>){

davetang

#!/bin/env perl

use strict;
use warnings;

my $usage = "Usage: $0 <infile.bed>\n";
my $infile = shift or die $usage;

my %bed = ();

davetang

#!/bin/env perl

use strict;
use warnings;

my $usage = "Usage: $0 <old_dir> <new_dir>\n";
my $old = shift or die $usage;
my $new = shift or die $usage;

my %current = ();

davetang

#!/usr/bin/env perl

use strict;
use warnings;

=head1 NAME

This scripts converts a psl file into a bed file written by Dave Tang.

=head1 SYNOPSIS