run_step0.pl

run_step0.pl

#!/usr/bin/env perl

# runs step 0 on all chromosomes
# produces the group files and the tarballed
# sets for running step1 and step 2 on

use strict;

# create and store distributions for the top 25 models from permutation testing
# for both the model p-value and interaction p-value

my $PRGM_NAME = "run_step0.pl";

my $step0script = '/scratch/username/impute/impute_step0.sh'; #CHANGE

# Subroutine: usage
# Displays current version date and usage
sub usage{
  print "\nusage:\t\t$PRGM_NAME <basename, not including .bed/bim/fam>\n\n";
  print "example:\t$PRGM_NAME mydata\n\n";
}

# subroutine: check_args
# Checks number of arguments passed in and returns name of pedigree file.
sub check_args{
  if(@ARGV != 1)
  { usage();
    exit;}

  return @ARGV;
}

my ($beginbase) = check_args();

for(my $i=1; $i<=22; $i++){
  my $basefile = "$beginbase$i";
  my $outbase = "$beginbase" . "_chr$i";
  print "$step0script $basefile $outbase\n";
  system("$step0script $basefile $outbase");
}