Created
November 12, 2010 19:57
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run_step1.pl
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#!/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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