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@stephenturner
Created November 12, 2010 19:57
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run_step1.pl
#!/usr/bin/env perl
# runs step 1 on all chromosomes
# produces the input for step 2 results
# submits a pbs job for every chromosome specified
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_step1.pl";
my $pbs = '/scratch/username/impute/impute_1000genomes.pbs'; #CHANGE
my $pbs_himemory = '/scratch/username/impute/impute_1000genomes_himem.pbs'; #CHANGE
# Subroutine: usage
# Displays current version date and usage
sub usage{
print "\nusage:\t\t$PRGM_NAME <basename>\n\n";
print "example:\t$PRGM_NAME hdlmarsh \n\n";
}
# subroutine: check_args
# Checks number of arguments passed in and returns name of pedigree file.
sub check_args{
if(@ARGV != 1)
{ usage();
exit;}
return @ARGV;
}
my ($basename) = check_args();
for(my $i=1; $i<=22; $i++){
# check that tarball exists for this chromosome
my @files = glob("*chr${i}_step0.tar.gz");
if(@files > 0){
print "submitting job for chromosome $i\n";
system("qsub $pbs_himemory -v PREFIX=$basename,CHR=$i") if $i<=2;
system("qsub $pbs -v PREFIX=$basename,CHR=$i") if $i>2;
}
}
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