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Copy pathmsgUpdateParentals.pl
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executable file
·185 lines (168 loc) · 9.51 KB
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#!/usr/bin/perl -w
use strict;
use lib qw(./msg .);
use Utils;
print "\nMSG - Update Parentals\n";
my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst)=localtime(time);
printf "%4d-%02d-%02d %02d:%02d:%02d\n\n", $year+1900,$mon+1,$mday,$hour,$min,$sec;
### Make sure all required dependencies are installed
&Utils::test_dependencies();
### Default parameters
### All of these parameters are required
my %default_params = (
bwaindex1 => 'bwtsw',
bwaindex2 => 'bwtsw',
cluster => '1',
threads => '8',
min_coverage => '2',
max_coverage_exceeded_state => 'N',
addl_qsub_option_for_exclusive_node => '',
addl_qsub_option_for_pe => '',
custom_qsub_options_for_all_cmds => '',
bwa_alg => 'aln',
bwa_threads => '1',
use_stampy => '0',
stampy_premap_w_bwa => '1',
stampy_pseudo_threads => '0',
quality_trim_reads_thresh => '0',
quality_trim_reads_consec => '30',
parent1_stampy_substitution_rate => '0.001',
parent2_stampy_substitution_rate => '0.001',
parent1_mapq_filter => '0',
parent2_mapq_filter => '0',
debug => '0',
);
my $params = Utils::parse_config('update.cfg', \%default_params);
# Validation of Required parameters
if (!((exists $params->{'parent1'} && exists $params->{'parent1_reads'}) || (exists $params->{'parent2'} && exists $params->{'parent2_reads'}))) {
die "Missing Parameters: parent1 and parent1_reads and/or parent2 and parent2_reads";
}
if (exists $params->{'parent1'}) {
Utils::validate_config($params, qw( parent1 parent1_reads));
}
if (exists $params->{'parent2'}) {
Utils::validate_config($params, qw( parent2 parent2_reads));
}
my %params = %$params;
####################################################################################################
if (exists $params{'parent1_reads'}) {
$params{'update_minQV'} = 1 unless (exists $params{'update_minQV'});
open (OUT,'>msgRunU0-1.sh');
print OUT "/bin/hostname\n/bin/date\n" .
'perl msg/msg.pl ' .
' --update ' .
' --parent1 ' . $params{'parent1'} .
' --update_minQV ' . $params{'update_minQV'} .
' --min_coverage ' . $params{'min_coverage'} .
' --max_coverage_exceeded_state ' . $params{'max_coverage_exceeded_state'} .
' --parent1-reads ' . $params{'parent1_reads'} .
' --bwaindex1 ' . $params{'bwaindex1'} .
' --bwaindex2 ' . $params{'bwaindex2'} .
' --bwa_alg ' . $params{'bwa_alg'} .
' --bwa_threads ' . $params{'bwa_threads'} .
' --use_stampy ' . $params{'use_stampy'} .
' --stampy_premap_w_bwa ' . $params{'stampy_premap_w_bwa'} .
' --stampy_pseudo_threads ' . $params{'stampy_pseudo_threads'} .
' --cluster ' . $params{'cluster'} .
' --quality_trim_reads_thresh ' . $params{'quality_trim_reads_thresh'} .
' --quality_trim_reads_consec ' . $params{'quality_trim_reads_consec'} .
' --parent_stampy_substitution_rate ' . $params{'parent1_stampy_substitution_rate'} .
' --parent_mapq_filter ' . $params{'parent1_mapq_filter'} .
' --debug ' . $params{'debug'}
;
#Add on optional arguments
if (defined $params{'max_coverage_stds'}) {
print OUT ' --max_coverage_stds ' . $params{'max_coverage_stds'};
}
if ($params{'addl_qsub_option_for_pe'}) {
print OUT ' --addl_qsub_option_for_pe pe';
}
if ($params{'custom_qsub_options_for_all_cmds'}) {
print OUT ' --custom_qsub_options_for_all_cmds "' . &Utils::strip($params{'custom_qsub_options_for_all_cmds'}) .'"';
}
print OUT " || exit 100\n";
close OUT;
&Utils::system_call("chmod 755 msgRunU0-1.sh");
$params{'parent1'} .= '.msg.updated.fasta';
}
if (exists $params{'parent2_reads'}) {
$params{'update_minQV'} = 1 unless (exists $params{'update_minQV'});
open (OUT,'>msgRunU0-2.sh');
print OUT "/bin/hostname\n/bin/date\n" .
'perl msg/msg.pl ' .
' --update ' .
' --parent2 ' . $params{'parent2'} .
' --update_minQV ' . $params{'update_minQV'} .
' --min_coverage ' . $params{'min_coverage'} .
' --max_coverage_exceeded_state ' . $params{'max_coverage_exceeded_state'} .
' --parent2-reads ' . $params{'parent2_reads'} .
' --bwaindex1 ' . $params{'bwaindex1'} .
' --bwaindex2 ' . $params{'bwaindex2'} .
' --bwa_alg ' . $params{'bwa_alg'} .
' --bwa_threads ' . $params{'bwa_threads'} .
' --use_stampy ' . $params{'use_stampy'} .
' --stampy_premap_w_bwa ' . $params{'stampy_premap_w_bwa'} .
' --stampy_pseudo_threads ' . $params{'stampy_pseudo_threads'} .
' --cluster ' . $params{'cluster'} .
' --quality_trim_reads_thresh ' . $params{'quality_trim_reads_thresh'} .
' --quality_trim_reads_consec ' . $params{'quality_trim_reads_consec'} .
' --parent_stampy_substitution_rate ' . $params{'parent2_stampy_substitution_rate'} .
' --parent_mapq_filter ' . $params{'parent2_mapq_filter'} .
' --debug ' . $params{'debug'}
;
#Add on optional arguments
if (defined $params{'max_coverage_stds'}) {
print OUT ' --max_coverage_stds ' . $params{'max_coverage_stds'};
}
if ($params{'addl_qsub_option_for_pe'}) {
print OUT ' --addl_qsub_option_for_pe pe';
}
if ($params{'custom_qsub_options_for_all_cmds'}) {
print OUT ' --custom_qsub_options_for_all_cmds "' . &Utils::strip($params{'custom_qsub_options_for_all_cmds'}) .'"';
}
print OUT " || exit 100\n";
close OUT;
&Utils::system_call("chmod 755 msgRunU0-2.sh");
$params{'parent2'} .= '.msg.updated.fasta';
}
####################################################################################################
mkdir "msgUpdateParentalsOut.$$" unless (-d "msgUpdateParentalsOut.$$");
mkdir "msgUpdateParentalsError.$$" unless (-d "msgUpdateParentalsError.$$");
### Run jobs!
if (exists $params{'parent1_reads'} and exists $params{'parent2_reads'}) {
if ($params{'cluster'} != 0) {
&Utils::system_call("qsub -N msgRunU0-1.$$ $params{'addl_qsub_option_for_pe'}-cwd $params{'addl_qsub_option_for_exclusive_node'}$params{'custom_qsub_options_for_all_cmds'}-b y -V -sync n ./msgRunU0-1.sh") ;
&Utils::system_call("qsub -N msgRunU0-2.$$ $params{'addl_qsub_option_for_pe'}-cwd $params{'addl_qsub_option_for_exclusive_node'}$params{'custom_qsub_options_for_all_cmds'}-b y -V -sync n ./msgRunU0-2.sh") ;
#Cleanup - move output files to folders
&Utils::system_call("qsub -N msgRunU6.$$ -hold_jid msgRunU0-1.$$,msgRunU0-2.$$ -cwd $params{'custom_qsub_options_for_all_cmds'}-b y -V -sync n \"mv -f msgRunU*.${$}.e** msgUpdateParentalsError.$$; mv -f msgRunU*.${$}.pe** msgUpdateParentalsError.$$; mv -f msgRunU*.${$}.o* msgUpdateParentalsOut.$$; mv -f msgRunU*.${$}.po* msgUpdateParentalsOut.$$; mv -f *.trim.log msgUpdateParentalsOut.$$\"");
} else {
&Utils::system_call("./msgRunU0-1.sh > msgRunU0-1.$$.out 2> msgRunU0-1.$$.err") ;
&Utils::system_call("./msgRunU0-2.sh > msgRunU0-2.$$.out 2> msgRunU0-2.$$.err") ;
#Cleanup - move output files to folders
&Utils::system_call("mv -f msgRunU*.${$}.e** msgUpdateParentalsError.$$; mv -f msgRunU*.${$}.o* msgUpdateParentalsOut.$$; mv -f *.trim.log msgUpdateParentalsOut.$$");
}
} elsif ( exists $params{'parent1_reads'} ) {
if ($params{'cluster'} != 0) {
&Utils::system_call("qsub -N msgRunU0-1.$$ $params{'addl_qsub_option_for_pe'}-cwd $params{'addl_qsub_option_for_exclusive_node'}$params{'custom_qsub_options_for_all_cmds'}-b y -V -sync n ./msgRunU0-1.sh") ;
#Cleanup - move output files to folders
&Utils::system_call("qsub -N msgRunU6.$$ -hold_jid msgRunU0-1.$$ -cwd $params{'custom_qsub_options_for_all_cmds'}-b y -V -sync n \"mv -f msgRunU*.${$}.e** msgUpdateParentalsError.$$; mv -f msgRunU*.${$}.pe** msgUpdateParentalsError.$$; mv -f msgRunU*.${$}.o* msgUpdateParentalsOut.$$; mv -f msgRunU*.${$}.po* msgUpdateParentalsOut.$$; mv -f *.trim.log msgUpdateParentalsOut.$$\"");
} else {
&Utils::system_call("./msgRunU0-1.sh > msgRunU0-1.$$.out 2> msgRunU0-1.$$.err") ;
#Cleanup - move output files to folders
&Utils::system_call("mv -f msgRunU*.${$}.e** msgUpdateParentalsError.$$; mv -f msgRunU*.${$}.o* msgUpdateParentalsOut.$$; mv -f *.trim.log msgUpdateParentalsOut.$$");
}
} elsif ( exists $params{'parent2_reads'} ) {
if ($params{'cluster'} != 0) {
&Utils::system_call("qsub -N msgRunU0-2.$$ $params{'addl_qsub_option_for_pe'}-cwd $params{'addl_qsub_option_for_exclusive_node'}$params{'custom_qsub_options_for_all_cmds'}-b y -V -sync n ./msgRunU0-2.sh") ;
#Cleanup - move output files to folders
&Utils::system_call("qsub -N msgRunU6.$$ -hold_jid msgRunU0-2.$$ -cwd $params{'custom_qsub_options_for_all_cmds'}-b y -V -sync n \"mv -f msgRunU*.${$}.e** msgUpdateParentalsError.$$; mv -f msgRunU*.${$}.pe** msgUpdateParentalsError.$$; mv -f msgRunU*.${$}.o* msgUpdateParentalsOut.$$; mv -f msgRunU*.${$}.po* msgUpdateParentalsOut.$$; mv -f *.trim.log msgUpdateParentalsOut.$$\"");
} else {
&Utils::system_call("./msgRunU0-2.sh > msgRunU0-2.$$.out 2> msgRunU0-2.$$.err") ;
#Cleanup - move output files to folders
&Utils::system_call("mv -f msgRunU*.${$}.e** msgUpdateParentalsError.$$; mv -f msgRunU*.${$}.o* msgUpdateParentalsOut.$$; mv -f *.trim.log msgUpdateParentalsOut.$$");
}
}
print "\nNOTE: Output and error messages are located in: msgUpdateParentalsOut.$$ and msgUpdateParentalsError.$$ \n\n";
if (exists $params{'parent1_reads'}) { print "Output file is $params{'parent1'}\n";}
if (exists $params{'parent2_reads'}) { print "Output file is $params{'parent2'}\n";}
exit;