allelePval2minN

#!/usr/bin/perl

use warnings;
use strict;
use File::Basename;
use Getopt::Long;
use Pod::Usage;
use Cwd;
use Switch;

=head1 NAME

allelePval2minN

=head1 SYNOPSIS

 allelePval2minN [options] <>	

  -h help
  
  binomialChart.txt:
  0       1
	1       1
  col1: min n
  col2: p-value
  
  pval-cutoff-rnaseq.txt:
  HG00096 0.009286
	HG00100 0.009399
  col1: sample name
  col2: p value cut off for each (rnaseq) set
  
  Example:
     allelePval2minN -b binomialChart.txt pval-cutoff-rnaseq.txt
  
=head1 DESCRIPTION

=cut

#option variables
my $help;
my $bfile = '';

#initialize options
Getopt::Long::Configure ('bundling');

if(!GetOptions ('h'=>\$help, 'b=s'=>\$bfile) || scalar(@ARGV)!=1)
{
    if ($help)
    {
        pod2usage(-verbose => 2);
    }
    else
    {
        pod2usage(1);
    }
}

#************************************* p value cutoff *******************************
## input list
my $ifile = $ARGV[0];
open (INPUT, $ifile) || die "Cannot open $ifile: $!";

## print to STDOUT

#************************************* binomial Chart *******************************
# binomial chart
# col1 0-100 - assume a binomial n, and the probability that all are successes (or all are failures)
# col2 p value cutoff

## read file
open (BFILE, $bfile) || die "Cannot open $bfile: $!";
my @bees = <BFILE>;
chomp @bees;

## variable
my $minN;
my $maxP;

############## read input list ##############
while (<INPUT>)
{
	chomp $_;
	s/\r?\n?$//;
	
	my @fields = split(/\t/,$_);
	
	## take p value and loop binomial chart to compare
	for(my $i=0; $i<@bees; $i++)
	{
		if($fields[1] > $bees[$i])
		{
			$minN = $i;
			$maxP = $bees[$i];
			last;
		}
	}
	
	
	## output
	print "$fields[0]\t$fields[1]\t$minN\t$maxP\n";
	
	
} # while INPUT

close(BFILE);
close(INPUT);