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scafe.tool.cm.cluster
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#!/usr/bin/env perl
# This chunk of stuff was generated by App::FatPacker. To find the original
# file's code, look for the end of this BEGIN block or the string 'FATPACK'
BEGIN {
my %fatpacked;
s/^ //mg for values %fatpacked;
my $class = 'FatPacked::'.(0+\%fatpacked);
no strict 'refs';
*{"${class}::files"} = sub { keys %{$_[0]} };
if ($] < 5.008) {
*{"${class}::INC"} = sub {
if (my $fat = $_[0]{$_[1]}) {
my $pos = 0;
my $last = length $fat;
return (sub {
return 0 if $pos == $last;
my $next = (1 + index $fat, "\n", $pos) || $last;
$_ .= substr $fat, $pos, $next - $pos;
$pos = $next;
return 1;
});
}
};
}
else {
*{"${class}::INC"} = sub {
if (my $fat = $_[0]{$_[1]}) {
open my $fh, '<', \$fat
or die "FatPacker error loading $_[1] (could be a perl installation issue?)";
return $fh;
}
return;
};
}
unshift @INC, bless \%fatpacked, $class;
} # END OF FATPACK CODE
#====================================================================================================================================================#
#<use>
$|++; #---turn on the auto flush for the progress bar
no warnings 'utf8';
use warnings;
use strict;
use File::Path;
use File::Copy;
use File::Basename;
use File::Spec::Functions qw(rel2abs abs2rel);
use Time::HiRes qw( time );
use Getopt::Long 'HelpMessage';
use List::Util qw (sum shuffle min max);
use Cwd 'abs_path';
#<\use>
#====================================================================================================================================================#
#====================================================================================================================================================#
#<doc>
=head1 SYNOPSIS
5'-O~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AAA-3'
O~~~AA O~~ O~ O~~~~~~~AO~~~~~~~~A
O~~ O~~ O~~ O~~ O~O~~ O~~ O~~
O~~ O~~ O~ O~~ O~~ O~~
O~~ O~~ O~~ O~~ O~~~~~AA O~~~~~~A
O~~ O~~ O~~~~~A O~~ O~~ O~~
O~~ O~~ O~~ O~~ O~~ O~~ O~~ O~~
O~~~~A O~~~ O~~ O~~O~~ O~~~~~~~AA
┌─ᐅ 5'-O~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-3'
...===┴========================================================================================...
Single Cell Analysis of Five-prime End (SCAFE) Tool Suite
---> scafe.tool.cm.cluster <---
<--- tool, common mode, cluster ctss --->
Description:
This tool generate TSS cluster from a ctss bed file, using an external tool paraclu with user-defined cutoffs
Usage:
scafe.tool.cm.cluster [options] --cluster_ctss_bed_path --outputPrefix --outDir
--cluster_ctss_bed_path <required> [string] ctss file used for clustering,
"collapse" ctss file from scafe.tool.sc.bam_to_ctss.pl,
4th column is number of cells and 5th column is number UMI
--outputPrefix <required> [string] prefix for the output files
--outDir <required> [string] directory for the output files
--count_ctss_bed_path_list (optional) [string] comma delimited list of ctss bed file,
using for filtering of clusters based signal
(default=$cluster_ctss_bed_path)
--count_scope_bed_path (optional) [string] a bed file specify the scope for counting in $count_ctss_bed_path_list,
using for filtering of clusters based signal
(default=$cluster_ctss_bed_path)
--min_pos_count (optional) [integer] minimum counts per position, used for filtering the raw signal
in $cluster_ctss_bed_path before clustering (default = 1)
--min_cluster_cpm (optional) [float] minimum counts per million (cpm) for a cluster (default = 1e-5)
--min_summit_count (optional) [integer] minimum counts at the summit of a cluster (default = 3)
--min_cluster_count (optional) [integer] minimum counts within a cluster (default = 5)
--min_num_sample_expr_cluster (optional) [integer] minimum number of samples (or cells) detected at the
summit of a cluster (default = 3)
--min_num_sample_expr_summit (optional) [integer] minimum number of samples (or cells) detected within
of a cluster (default = 5)
--merge_dist (optional) [integer] maximum distance for merging closely located clusters,
-1 to turn off merging (default = -1)
--overwrite (optional) [yes/no] erase outDir/outputPrefix before running (default=no)
Dependencies:
paraclu
paraclu-cut.sh
bedtools
For demo, cd to SCAFE dir and run,
scafe.tool.cm.cluster \
--overwrite=yes \
--cluster_ctss_bed_path=./demo/output/sc.solo/bam_to_ctss/demo/bed/demo.collapse.ctss.bed.gz \
--outputPrefix=demo \
--outDir=./demo/output/sc.solo/cluster/
=head1 VERSION
v0.9.0-beta [March 20, 2021]
-Initial pre-release
v1.0.0 [June 6, 2022]
-parallelized part of the processes
=cut#
#<\doc>
#====================================================================================================================================================#
#====================================================================================================================================================#
#<lastCmdCalled>
#
# notCalledBefore
#
# notCalledBefore
#
#<\lastCmdCalled>
#====================================================================================================================================================#
#====================================================================================================================================================#
#<global>
my $scriptDirPath = dirname(rel2abs($0));
my $scriptAbsPath = abs_path($0);
my ($curntTimeStamp) = &timeStamp();#->1090
my $ARGVStr = join "\n", (¤tTime(), $scriptAbsPath, @ARGV);#->301
my $globalReadmeHsh_ref = {};
our $tmplog_fh;
#<\global>
#====================================================================================================================================================#
#====================================================================================================================================================#
{ #Main sections lexical scope starts
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 0_startingTasks
#
#<section ID="startingTasks" num="0">
my ($cluster_ctss_bed_path, $count_ctss_bed_path_list, $count_scope_bed_path, $min_cluster_cpm, $min_cluster_count, $min_pos_count, $min_summit_count, $merge_dist, $min_num_sample_expr_cluster, $min_num_sample_expr_summit, $outputPrefix, $outDir, $overwrite) = &readParameters();#->901
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 1_defineHardCodedParam
#
#<section ID="defineHardCodedParam" num="1">
my $paramTag = "$outputPrefix";
my $force_rerun = 'yes'; #---[2020/04/21 0:18] force to rerun paraclu even results exists
my @mkDirAry;
my $result_dir = "$outDir/$paramTag/"; push @mkDirAry, $result_dir;
system "rm -rf $result_dir" if ($overwrite eq 'yes');
my $resultParacluDir = "$result_dir/paraclu/"; push @mkDirAry, $resultParacluDir;
my $resultBedDir = "$result_dir/bed/"; push @mkDirAry, $resultBedDir;
my $resultPreMergeBedDir = "$result_dir/bed/pre_merge/"; push @mkDirAry, $resultPreMergeBedDir;
my $resultLogDir = "$result_dir/log/"; push @mkDirAry, $resultLogDir;
my $resultScriptDir = "$result_dir/script/"; push @mkDirAry, $resultScriptDir;
foreach my $dir (@mkDirAry) {system ("mkdir -pm 755 $dir");}
open $tmplog_fh, ">", "$result_dir/00_screen_log.$curntTimeStamp.log.txt";
&printStartOrFinishMessage("startMessage");#->867
&logCalledCMDAndScript($ARGVStr, $resultScriptDir, $scriptAbsPath);#->472
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 2_ReadInfoAndRun
#
#<section ID="ReadInfoAndRun" num="2">
my ($tabix_bin, $bgzip_bin, $bedtools_bin, $samtools_bin, $paraclu_bin, $cut_sh_path, $bedGraphToBigWig_bin, $bigWigAverageOverBed_bin) = &checkAllExecutable();#->201
my ($count_ctss_bed_hsh_ref) = &getCountCtssPath($count_ctss_bed_path_list, $count_scope_bed_path);#->319
my ($paraclu_input_path, $min_cluster_count_by_cpm) = &parseParacluInput($cluster_ctss_bed_path, $min_pos_count, $min_cluster_cpm, $resultParacluDir);#->584
my ($paraclu_bed_path) = &runParaclu($paraclu_input_path, $paraclu_bin, $cut_sh_path, $resultParacluDir, $resultPreMergeBedDir, $min_cluster_count, $min_cluster_count_by_cpm, $paramTag, $force_rerun);#->984
my ($paraclu_cluster_info_hsh_ref, $summit_bed_path) = &getTssClusterSummit($resultPreMergeBedDir, $paraclu_bed_path, $cluster_ctss_bed_path, $bedtools_bin, $paramTag);#->423
my ($tmp_merge_bed_file_path, $tssCluster_info_hsh_ref) = &mergeParacluClusters($bedtools_bin, $summit_bed_path, $merge_dist, $cluster_ctss_bed_path, $resultBedDir, $resultLogDir, $paramTag, $paraclu_cluster_info_hsh_ref, $min_summit_count);#->497
&getNumSampleExpressed($tmp_merge_bed_file_path, $tssCluster_info_hsh_ref, $count_ctss_bed_hsh_ref, $bedtools_bin);#->364
&printFinalBedAndLog($tmp_merge_bed_file_path, $tssCluster_info_hsh_ref, $resultBedDir, $resultLogDir, $paramTag, $min_num_sample_expr_cluster, $min_num_sample_expr_summit);#->641
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 3_finishingTasks
#
#<section ID="finishingTasks" num="3">
&printOutputFileListAndReadme($ARGVStr, $paramTag, $outDir);#->752
&printStartOrFinishMessage("finishMessage");#->867
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
} #Main sections lexical scope ends
#====================================================================================================================================================#
#====================================================================================================================================================#
#List of subroutines by category
#
# general [n=5]:
# currentTime, logCalledCMDAndScript, printStartOrFinishMessage
# readParameters, timeStamp
#
# log [n=1]:
# reportAndLogStatus
#
# output [n=1]:
# printOutputFileListAndReadme
#
# time [n=1]:
# timeStamp
#
# unassigned [n=8]:
# checkAllExecutable, getCountCtssPath, getNumSampleExpressed
# getTssClusterSummit, mergeParacluClusters, parseParacluInput
# printFinalBedAndLog, runParaclu
#
#====================================================================================================================================================#
sub checkAllExecutable {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|962
# appearInSub: >none
# primaryAppearInSection: 2_ReadInfoAndRun|150
# secondaryAppearInSection: >none
# input: none
# output: $bedGraphToBigWig_bin, $bedtools_bin, $bgzip_bin, $bigWigAverageOverBed_bin, $cut_sh_path, $paraclu_bin, $samtools_bin, $tabix_bin
# toCall: my ($tabix_bin, $bgzip_bin, $bedtools_bin, $samtools_bin, $paraclu_bin, $cut_sh_path, $bedGraphToBigWig_bin, $bigWigAverageOverBed_bin) = &checkAllExecutable();
# calledInLine: 153
#....................................................................................................................................................#
my $dirPath = dirname(rel2abs($0));
my $tabix_bin = "$dirPath/../resources/bin/tabix/tabix";
my $bgzip_bin = "$dirPath/../resources/bin/bgzip/bgzip";
my $bedtools_bin = "$dirPath/../resources/bin/bedtools/bedtools";
my $samtools_bin = "$dirPath/../resources/bin/samtools/samtools";
my $paraclu_bin = "$dirPath/../resources/bin/paraclu/paraclu";
my $cut_sh_path = "$dirPath/../resources/bin/paraclu/paraclu-cut.sh";
my $bedGraphToBigWig_bin = "$dirPath/../resources/bin/bedGraphToBigWig/bedGraphToBigWig";
my $bigWigAverageOverBed_bin = "$dirPath/../resources/bin/bigWigAverageOverBed/bigWigAverageOverBed";
&reportAndLogStatus("Checking all SCAFE executables", 10, "\n");#->962
{
my $stdOut = `$tabix_bin --version 2>&1`;
if ($stdOut =~ m/tabix \(htslib\) (\S+)/) {
&reportAndLogStatus("Checking: tabix version: $1", 0, "\n");#->962
} else {
die "tabix is not installed properly. Quitting.\n";
}
}
{
my $stdOut = `$bgzip_bin --version 2>&1`;
if ($stdOut =~ m/bgzip \(htslib\) (\S+)/) {
&reportAndLogStatus("Checking: bgzip version: $1", 0, "\n");#->962
} else {
die "bgzip is not installed properly. Quitting.\n";
}
}
{
my $stdOut = `$bedtools_bin --version 2>&1`;
if ($stdOut =~ m/bedtools v(\S+)/) {
&reportAndLogStatus("Checking: bedtools version: $1", 0, "\n");#->962
} else {
die "bedtools is not installed properly. Quitting.\n";
}
}
{
my $stdOut = `$samtools_bin 2>&1`;
if ($stdOut =~ m/\s+(Version: \S+)\s+/) {
&reportAndLogStatus("Checking: samtools version: $1", 0, "\n");#->962
} else {
die "samtools is not installed properly. Quitting.\n";
}
}
{
my $stdOut = `$paraclu_bin 2>&1`;
if ($stdOut =~ m/paraclu: I need a minValue and a fileName/) {
&reportAndLogStatus("Checking: paraclu found.", 0, "\n");#->962
} else {
die "paraclu is not installed properly. Quitting.\n";
}
}
{
my $stdOut = `$cut_sh_path 55C7128A 2>&1`;
if ($stdOut =~ m/awk:/) {
&reportAndLogStatus("Checking: paraclu-cut found.", 0, "\n");#->962
} else {
die "paraclu-cut is not installed properly. Quitting.\n";
}
}
{
my $stdOut = `$bedGraphToBigWig_bin 2>&1`;
if ($stdOut =~ m/bedGraphToBigWig v (\S+)/) {
&reportAndLogStatus("Checking: bedGraphToBigWig version: $1", 0, "\n");#->962
} else {
die "bedGraphToBigWig not installed properly. Quitting.\n";
}
}
{
my $stdOut = `$bigWigAverageOverBed_bin 2>&1`;
if ($stdOut =~ m/bigWigAverageOverBed v(\S+)/) {
&reportAndLogStatus("Checking: bigWigAverageOverBed version: $1", 0, "\n");#->962
} else {
die "bigWigAverageOverBed is not installed properly. Quitting.\n";
}
}
return ($tabix_bin, $bgzip_bin, $bedtools_bin, $samtools_bin, $paraclu_bin, $cut_sh_path, $bedGraphToBigWig_bin, $bigWigAverageOverBed_bin);
}
sub currentTime {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: >none
# appearInSub: printStartOrFinishMessage|867, reportAndLogStatus|962
# primaryAppearInSection: >none
# secondaryAppearInSection: 1_defineHardCodedParam|127, 3_finishingTasks|165
# input: none
# output: $runTime
# toCall: my ($runTime) = ¤tTime();
# calledInLine: 108, 883, 887, 892, 896, 978, 979
#....................................................................................................................................................#
my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst)=localtime(time);
my $runTime = sprintf "%04d-%02d-%02d %02d:%02d", $year+1900, $mon+1,$mday,$hour,$min;
return $runTime;
}
sub getCountCtssPath {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|962
# appearInSub: >none
# primaryAppearInSection: 2_ReadInfoAndRun|150
# secondaryAppearInSection: >none
# input: $count_ctss_bed_path_list, $count_scope_bed_path
# output: $count_ctss_bed_hsh_ref
# toCall: my ($count_ctss_bed_hsh_ref) = &getCountCtssPath($count_ctss_bed_path_list, $count_scope_bed_path);
# calledInLine: 154
#....................................................................................................................................................#
my ($count_ctss_bed_path_list, $count_scope_bed_path) = @_;
&reportAndLogStatus("checking count_ctss_bed_path_list", 10, "\n");#->962
my $count_ctss_bed_hsh_ref = {};
if (defined $count_ctss_bed_path_list) {
foreach my $count_ctss_bed_path (split /\,/, $count_ctss_bed_path_list) {
if (-s $count_ctss_bed_path) {
if (exists $count_ctss_bed_hsh_ref->{$count_ctss_bed_path}) {
&reportAndLogStatus("WARNING: $count_ctss_bed_path appeared more than once.", 10, "\n");#->962
}
$count_ctss_bed_hsh_ref->{'count_ctss_bed_path'}{$count_ctss_bed_path}++;
} else {
die "count_ctss_bed_path: $count_ctss_bed_path does not exist\n";
}
}
my $num_ctss_count_bed = keys %{$count_ctss_bed_hsh_ref->{'count_ctss_bed_path'}};
&reportAndLogStatus("stored $num_ctss_count_bed ctss bed for counting num sample expressed", 10, "\n");#->962
} else {
&reportAndLogStatus("num sample expressed will not be used for filtering", 10, "\n");#->962
}
if (defined $count_scope_bed_path) {
if (-s $count_scope_bed_path) {
$count_ctss_bed_hsh_ref->{'count_scope_bed_path'} = $count_scope_bed_path;
} else {
die "count_scope_bed_path: $count_scope_bed_path does not exist\n";
}
}
return ($count_ctss_bed_hsh_ref);
}
sub getNumSampleExpressed {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|962
# appearInSub: >none
# primaryAppearInSection: 2_ReadInfoAndRun|150
# secondaryAppearInSection: >none
# input: $bedtools_bin, $count_ctss_bed_hsh_ref, $tmp_merge_bed_file_path, $tssCluster_info_hsh_ref
# output:
# toCall: &getNumSampleExpressed($tmp_merge_bed_file_path, $tssCluster_info_hsh_ref, $count_ctss_bed_hsh_ref, $bedtools_bin);
# calledInLine: 159
#....................................................................................................................................................#
my ($tmp_merge_bed_file_path, $tssCluster_info_hsh_ref, $count_ctss_bed_hsh_ref, $bedtools_bin) = @_;
if (exists $count_ctss_bed_hsh_ref->{'count_ctss_bed_path'}) {
foreach my $count_ctss_bed_path (keys %{$count_ctss_bed_hsh_ref->{'count_ctss_bed_path'}}) {
my ($fileName, $fileDir, $fileSuffix) = fileparse($count_ctss_bed_path, qr/\.[^.]*/);
&reportAndLogStatus("counting num sample expressed in $fileName$fileSuffix", 10, "\n");#->962
my $bedtools_cmd;
if (exists $count_ctss_bed_hsh_ref->{'count_scope_bed_path'}) {
&reportAndLogStatus("couting within scope of count_scope_bed_path", 10, "\n");#->962
my $count_scope_bed_path = $count_ctss_bed_hsh_ref->{'count_scope_bed_path'};
$bedtools_cmd = "$bedtools_bin intersect -sorted -s -wa -a $count_ctss_bed_path -b $count_scope_bed_path | $bedtools_bin intersect -sorted -s -wo -a $tmp_merge_bed_file_path -b stdin";
} else {
$bedtools_cmd = "$bedtools_bin intersect -sorted -s -wo -a $tmp_merge_bed_file_path -b $count_ctss_bed_path";
}
#print "$bedtools_cmd\n";
open BEDTOOLS, "$bedtools_cmd | cut -f 4,8,15,16,17 |";
while (<BEDTOOLS>) {
#print $_;
chomp;
#chr1 7973224 7973330 chr1_7973224_7973330_- 1727 - 7973316 7973317 31,120,180 1 106 0 chr1 7973279 7973280 11 11 - 1
#chr1 7973224 7973330 chr1_7973224_7973330_- 1727 - 7973316 7973317 31,120,180 1 106 0 chr1 7973280 7973281 1 1 - 1
#chr1 7973224 7973330 chr1_7973224_7973330_- 1727 - 7973316 7973317 31,120,180 1 106 0 chr1 7973281 7973282 137 168 - 1
my ($tssClusterID, $summit_pos, $ctss_pos, $num_sample_expr) = split /\t/;
if (exists $tssCluster_info_hsh_ref->{$tssClusterID}) {
$tssCluster_info_hsh_ref->{$tssClusterID}{'num_sample_expr_cluster'} += $num_sample_expr;
if ($summit_pos == $ctss_pos) {
$tssCluster_info_hsh_ref->{$tssClusterID}{'num_sample_expr_summit'} += $num_sample_expr;
}
} else {
die "tssClusterID $tssClusterID does not exists in $tssCluster_info_hsh_ref\n";
}
}
close BEDTOOLS;
}
} else {
&reportAndLogStatus("No count_ctss_bed_path. Assigning num_sample_expr_cluster -1 to all tssClusters", 10, "\n");#->962
foreach my $tssClusterID (keys %{$tssCluster_info_hsh_ref}) {
$tssCluster_info_hsh_ref->{$tssClusterID}{'num_sample_expr_cluster'} = -1;
$tssCluster_info_hsh_ref->{$tssClusterID}{'num_sample_expr_summit'} = -1;
}
}
return ();
}
sub getTssClusterSummit {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|962
# appearInSub: >none
# primaryAppearInSection: 2_ReadInfoAndRun|150
# secondaryAppearInSection: >none
# input: $bedtools_bin, $cluster_ctss_bed_path, $paraclu_bed_path, $paramTag, $resultPreMergeBedDir
# output: $paraclu_cluster_info_hsh_ref, $summit_bed_path
# toCall: my ($paraclu_cluster_info_hsh_ref, $summit_bed_path) = &getTssClusterSummit($resultPreMergeBedDir, $paraclu_bed_path, $cluster_ctss_bed_path, $bedtools_bin, $paramTag);
# calledInLine: 157
#....................................................................................................................................................#
my ($resultPreMergeBedDir, $paraclu_bed_path, $cluster_ctss_bed_path, $bedtools_bin, $paramTag) = @_;
my $paraclu_cluster_info_hsh_ref = {};
&reportAndLogStatus("getting summit position", 10, "\n");#->962
my $bedtools_cmd = "$bedtools_bin intersect -sorted -a $paraclu_bed_path -b $cluster_ctss_bed_path -s -wao";
open BEDTOOLS, "$bedtools_cmd |";
while (<BEDTOOLS>) {
chomp;
my ($chrom, $chromStart, $chromEnd, $paraclu_clusterID, $stability, $strand, undef, undef, $ctss_pos, undef, $ctss_read) = split /\t/;
if (not exists $paraclu_cluster_info_hsh_ref->{$paraclu_clusterID}) {
$paraclu_cluster_info_hsh_ref->{$paraclu_clusterID} = [$chrom, $chromStart, $chromEnd, $strand, $ctss_read, $ctss_pos, $ctss_read, $stability];
} else {
$paraclu_cluster_info_hsh_ref->{$paraclu_clusterID}[-4] += $ctss_read;
if ($ctss_read > $paraclu_cluster_info_hsh_ref->{$paraclu_clusterID}[-2]) {
$paraclu_cluster_info_hsh_ref->{$paraclu_clusterID}[-2] = $ctss_read;
$paraclu_cluster_info_hsh_ref->{$paraclu_clusterID}[-3] = $ctss_pos;
}
}
}
close BEDTOOLS;
my $summit_bed_path = "$resultPreMergeBedDir/$paramTag.pre_merge.tssCluster.summit.bed.gz";
$globalReadmeHsh_ref->{$summit_bed_path}{'description'} = "bed file of parsed paraclu cluster summit after 'cutting'";
&reportAndLogStatus("printing paraclu summit bed", 10, "\n");#->962
open SUMMIT, "| sort -k1,1 -k2,2n | gzip -c >$summit_bed_path";
foreach my $paraclu_clusterID (keys %{$paraclu_cluster_info_hsh_ref}) {
my ($chrom, undef, undef, $strand, $num_read, $summit_pos, $summit_read, $stability) = @{$paraclu_cluster_info_hsh_ref->{$paraclu_clusterID}};
my $chromStart = $summit_pos-1;
my $chromEnd = $summit_pos;
print SUMMIT join "", (join "\t", ($chrom, $chromStart, $chromEnd, $paraclu_clusterID, $summit_read, $strand)), "\n";
}
close SUMMIT;
return ($paraclu_cluster_info_hsh_ref, $summit_bed_path);
}
sub logCalledCMDAndScript {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 1_defineHardCodedParam|127
# secondaryAppearInSection: >none
# input: $ARGVStr, $resultScriptDir, $scriptAbsPath
# output:
# toCall: &logCalledCMDAndScript($ARGVStr, $resultScriptDir, $scriptAbsPath);
# calledInLine: 145
#....................................................................................................................................................#
my ($ARGVStr, $resultScriptDir, $scriptAbsPath) = @_;
my $cpScriptPath = "$resultScriptDir/script.ran.pl";
my $calledCMDPath = "$resultScriptDir/called.cmd.txt";
system "cp -f $scriptAbsPath $cpScriptPath";
system "chmod 0444 $cpScriptPath"; #---[07/03/2014 18:02] make it read-only to make sure there'll be accodental change of parameters
open CALLEDCMD, ">", $calledCMDPath;
print CALLEDCMD join "", ($ARGVStr), "\n";
close CALLEDCMD;
return ();
}
sub mergeParacluClusters {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|962
# appearInSub: >none
# primaryAppearInSection: 2_ReadInfoAndRun|150
# secondaryAppearInSection: >none
# input: $bedtools_bin, $cluster_ctss_bed_path, $merge_dist, $min_summit_count, $paraclu_cluster_info_hsh_ref, $paramTag, $resultBedDir, $resultLogDir, $summit_bed_path
# output: $tmp_merge_bed_file_path, $tssCluster_info_hsh_ref
# toCall: my ($tmp_merge_bed_file_path, $tssCluster_info_hsh_ref) = &mergeParacluClusters($bedtools_bin, $summit_bed_path, $merge_dist, $cluster_ctss_bed_path, $resultBedDir, $resultLogDir, $paramTag, $paraclu_cluster_info_hsh_ref, $min_summit_count);
# calledInLine: 158
#....................................................................................................................................................#
my ($bedtools_bin, $summit_bed_path, $merge_dist, $cluster_ctss_bed_path, $resultBedDir, $resultLogDir, $paramTag, $paraclu_cluster_info_hsh_ref, $min_summit_count) = @_;
&reportAndLogStatus("merging distance = $merge_dist", 10, "\n");#->962
&reportAndLogStatus("minimum post-merge summit count = $min_summit_count", 10, "\n");#->962
&reportAndLogStatus("start merging clusters", 10, "\n");#->962
&reportAndLogStatus("merging at $merge_dist nt", 10, "\n");#->962
my $tmp_merge_dir = "$resultBedDir/tmp_merged/";
system ("mkdir -pm 755 $tmp_merge_dir");
my $tmp_merge_bed_file_path = "$tmp_merge_dir/$paramTag.tssCluster.tmp_merged.bed.gz";
open OUTBED, "| sort -k1,1 -k2,2n | gzip -c >$tmp_merge_bed_file_path";
$globalReadmeHsh_ref->{$tmp_merge_bed_file_path}{'description'} = "bed file of the final tssCluster (post merging and filtering by summit count). Score column refers to number of read";
my $tssCluster_info_hsh_ref = {};
open BEDTOOLS, "$bedtools_bin merge -i $summit_bed_path -s -d $merge_dist -c 4 -o distinct | cut -f 4 |";
while (<BEDTOOLS>) {
chomp;
my ($paraclu_clusterID_str) = $_;
my $merged_cluster_info_hsh_ref = {};
my $num_read = 0;
foreach my $paraclu_clusterID (split /,/) {
die "paraclu_clusterID $paraclu_clusterID does not exists\n" if not exists $paraclu_cluster_info_hsh_ref->{$paraclu_clusterID};
my ($indiv_chrom, $indiv_chromStart, $indiv_chromEnd, $indiv_strand, $indiv_num_read, $indiv_summit_pos, $indiv_summit_read, $indiv_stability) = @{$paraclu_cluster_info_hsh_ref->{$paraclu_clusterID}};
push @{$merged_cluster_info_hsh_ref->{'bound'}}, ($indiv_chromStart, $indiv_chromEnd);
push @{$merged_cluster_info_hsh_ref->{'stability'}}, $indiv_stability;
$merged_cluster_info_hsh_ref->{'chrom'} = $indiv_chrom;
$merged_cluster_info_hsh_ref->{'strand'} = $indiv_strand;
$merged_cluster_info_hsh_ref->{'summit'}{$indiv_summit_read} = $indiv_summit_pos;
$num_read += $indiv_num_read;
}
@{$merged_cluster_info_hsh_ref->{'bound'}} = sort {$a<=>$b} @{$merged_cluster_info_hsh_ref->{'bound'}};
my $stability = sum(@{$merged_cluster_info_hsh_ref->{'stability'}})/@{$merged_cluster_info_hsh_ref->{'stability'}};
$stability = sprintf "%.5f", $stability;
my @summit_read_ary = sort {$a<=>$b} (keys %{$merged_cluster_info_hsh_ref->{'summit'}});
my $summit_read = $summit_read_ary[-1];
my $summit_pos = $merged_cluster_info_hsh_ref->{'summit'}{$summit_read};
if ($summit_read >= $min_summit_count) {
my $num_paraclu_cluster = keys %{$merged_cluster_info_hsh_ref->{'summit'}};
my $chrom = $merged_cluster_info_hsh_ref->{'chrom'};
my $chromStart = $merged_cluster_info_hsh_ref->{'bound'}[0];
my $chromEnd = $merged_cluster_info_hsh_ref->{'bound'}[-1];
my $strand = $merged_cluster_info_hsh_ref->{'strand'};
my $tssClusterID = join "_", ($chrom, $chromStart, $chromEnd, $strand);
my $size = $chromEnd - $chromStart;
my $thickStart = $summit_pos - 1;
my $thickEnd = $summit_pos;
my $itemRgb = "227,26,28";
$itemRgb = "31,120,180" if $strand eq '-';
my $blockCount = 1;
my $blockSizes = $size;
my $blockStarts = 0;
$tssCluster_info_hsh_ref->{$tssClusterID}{'chrom'} = $chrom;
$tssCluster_info_hsh_ref->{$tssClusterID}{'num_paraclu_cluster'} = $num_paraclu_cluster;
$tssCluster_info_hsh_ref->{$tssClusterID}{'size'} = $size;
$tssCluster_info_hsh_ref->{$tssClusterID}{'stability'} = $stability;
$tssCluster_info_hsh_ref->{$tssClusterID}{'num_read'} = $num_read;
$tssCluster_info_hsh_ref->{$tssClusterID}{'summit_pos'} = $summit_pos;
$tssCluster_info_hsh_ref->{$tssClusterID}{'summit_read'} = $summit_read;
$tssCluster_info_hsh_ref->{$tssClusterID}{'num_sample_expr_cluster'} = 0;
$tssCluster_info_hsh_ref->{$tssClusterID}{'num_sample_expr_summit'} = 0;
print OUTBED join "", (join "\t", ($chrom, $chromStart, $chromEnd, $tssClusterID, $num_read, $strand, $thickStart, $thickEnd, $itemRgb, $blockCount, $blockSizes, $blockStarts)), "\n";
}
}
close BEDTOOLS;
close OUTBED;
return ($tmp_merge_bed_file_path, $tssCluster_info_hsh_ref);
}
sub parseParacluInput {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|962
# appearInSub: >none
# primaryAppearInSection: 2_ReadInfoAndRun|150
# secondaryAppearInSection: >none
# input: $cluster_ctss_bed_path, $min_cluster_cpm, $min_pos_count, $resultParacluDir
# output: $min_cluster_count_by_cpm, $paraclu_input_path
# toCall: my ($paraclu_input_path, $min_cluster_count_by_cpm) = &parseParacluInput($cluster_ctss_bed_path, $min_pos_count, $min_cluster_cpm, $resultParacluDir);
# calledInLine: 155
#....................................................................................................................................................#
my ($cluster_ctss_bed_path, $min_pos_count, $min_cluster_cpm, $resultParacluDir) = @_;
my %itemForThrHsh = ();
my $threadID = 1;
my $paraclu_input_path = "$resultParacluDir/paraclu.input.txt.gz";
$globalReadmeHsh_ref->{$paraclu_input_path}{'description'} = "Input for paraclu";
my $total_count = 0;
&reportAndLogStatus("Parsing paraclu input with min_pos_count = $min_pos_count", 10, "\n");#->962
&reportAndLogStatus("Position with counts < $min_pos_count will be removed", 10, "\n");#->962
open PARACLUINPUT, "| gzip -c >$paraclu_input_path";
if ($cluster_ctss_bed_path =~ m/\.gz$/) {
open (FILEIN, " gzip -dc $cluster_ctss_bed_path|");
} else {
open (FILEIN, "<", $cluster_ctss_bed_path);
}
while (<FILEIN>) {
next if $_ =~ m/^#/;
chomp;
my @bedAry = split /\t/;
my $chrom = $bedAry[0];
my $pos = $bedAry[2];
my $score = $bedAry[4];
my $strand = $bedAry[5];
$total_count += $score;
if ($score >= $min_pos_count) {
print PARACLUINPUT join "", (join "\t", ($chrom, $strand, $pos, $score)), "\n";
}
}
close FILEIN;
close PARACLUINPUT;
my $total_count_millions = sprintf "%.5f", $total_count/1000000;
my $min_cluster_count_by_cpm = sprintf "%.0f", $min_cluster_cpm*$total_count_millions;
&reportAndLogStatus("total_count = $total_count_millions millions", 10, "\n");#->962
&reportAndLogStatus("min_cluster_cpm = $min_cluster_cpm", 10, "\n");#->962
return ($paraclu_input_path, $min_cluster_count_by_cpm);
}
sub printFinalBedAndLog {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|962
# appearInSub: >none
# primaryAppearInSection: 2_ReadInfoAndRun|150
# secondaryAppearInSection: >none
# input: $min_num_sample_expr_cluster, $min_num_sample_expr_summit, $paramTag, $resultBedDir, $resultLogDir, $tmp_merge_bed_file_path, $tssCluster_info_hsh_ref
# output:
# toCall: &printFinalBedAndLog($tmp_merge_bed_file_path, $tssCluster_info_hsh_ref, $resultBedDir, $resultLogDir, $paramTag, $min_num_sample_expr_cluster, $min_num_sample_expr_summit);
# calledInLine: 160
#....................................................................................................................................................#
my ($tmp_merge_bed_file_path, $tssCluster_info_hsh_ref, $resultBedDir, $resultLogDir, $paramTag, $min_num_sample_expr_cluster, $min_num_sample_expr_summit) = @_;
&reportAndLogStatus("printing final cluster bed and log", 10, "\n");#->962
my $read_cut_ary_ref = [(1..15),30,40,50,60,70,80,90,100];
my $size_cut_ary_ref = [5,10,15,20,25,35,40,45,50,60,70,80,90,100,125,150,175,200,300,400,500];
my $interval_hsh_ref = {
'cluster_read_less_than' => $read_cut_ary_ref,
'summit_read_less_than' => $read_cut_ary_ref,
'num_sample_expr_cluster_less_than' => $read_cut_ary_ref,
'num_sample_expr_summit_less_than' => $read_cut_ary_ref,
'size_greater_than' => $size_cut_ary_ref,
},
my $count_hsh_ref = {};
foreach my $param (keys %{$interval_hsh_ref}) {
foreach my $cutoff (@{$interval_hsh_ref->{$param}}) {
$count_hsh_ref->{$param}{$cutoff} = 0;
}
};
my $out_bed_file_path = "$resultBedDir/$paramTag.tssCluster.bed.gz";
my $out_log_file_path = "$resultLogDir/$paramTag.tssCluster.log.tsv.gz";
open OUTBED, "| gzip -c >$out_bed_file_path";
open OUTLOG, "| gzip -c >$out_log_file_path";
print OUTLOG join "", (join "\t", ('tssClusterID', 'chrom', 'num_paraclu_cluster', 'size', 'num_read', 'summit_pos', 'summit_read', 'num_sample_expr_cluster', 'num_sample_expr_summit', 'stability')), "\n";
$globalReadmeHsh_ref->{$out_log_file_path}{'description'} = "information of the final tssCluster (post merging and filtering by summit count)";
$globalReadmeHsh_ref->{$out_bed_file_path}{'description'} = "bed file of the final tssCluster (post merging and filtering by summit count and num sample expressed). Score column refers to number of read";
if ($tmp_merge_bed_file_path =~ m/\.gz$/) {
open (FILEIN, " gzip -dc $tmp_merge_bed_file_path|");
} else {
open (FILEIN, "<", $tmp_merge_bed_file_path);
}
my $total_num = 0;
while (<FILEIN>) {
chomp;
my @splt = split /\t/;
my $tssClusterID = $splt[3];
die "tssClusterID $tssClusterID does not exists\n" if not exists $tssCluster_info_hsh_ref->{$tssClusterID};
my $num_sample_expr_cluster = $tssCluster_info_hsh_ref->{$tssClusterID}{'num_sample_expr_cluster'};
my $num_sample_expr_summit = $tssCluster_info_hsh_ref->{$tssClusterID}{'num_sample_expr_summit'};
next if ($num_sample_expr_cluster != -1 and $num_sample_expr_cluster < $min_num_sample_expr_cluster);
next if ($num_sample_expr_summit != -1 and $num_sample_expr_summit < $min_num_sample_expr_summit);
$total_num++;
my $chrom = $tssCluster_info_hsh_ref->{$tssClusterID}{'chrom'};
my $num_paraclu_cluster = $tssCluster_info_hsh_ref->{$tssClusterID}{'num_paraclu_cluster'};
my $size = $tssCluster_info_hsh_ref->{$tssClusterID}{'size'};
my $num_read = $tssCluster_info_hsh_ref->{$tssClusterID}{'num_read'};
my $summit_pos = $tssCluster_info_hsh_ref->{$tssClusterID}{'summit_pos'};
my $summit_read = $tssCluster_info_hsh_ref->{$tssClusterID}{'summit_read'};
my $stability = $tssCluster_info_hsh_ref->{$tssClusterID}{'stability'};
foreach my $param (keys %{$count_hsh_ref}) {
foreach my $cutoff (keys %{$count_hsh_ref->{$param}}) {
if ($param eq 'cluster_read_less_than') {
$count_hsh_ref->{$param}{$cutoff}++ if $num_read < $cutoff;
} elsif ($param eq 'summit_read_less_than') {
$count_hsh_ref->{$param}{$cutoff}++ if $summit_read < $cutoff;
} elsif ($param eq 'num_sample_expr_summit_less_than') {
$count_hsh_ref->{$param}{$cutoff}++ if $num_sample_expr_summit < $cutoff;
} elsif ($param eq 'num_sample_expr_cluster_less_than') {
$count_hsh_ref->{$param}{$cutoff}++ if $num_sample_expr_cluster < $cutoff;
} elsif ($param eq 'size_greater_than') {
$count_hsh_ref->{$param}{$cutoff}++ if $size > $cutoff;
} else {
die;
}
}
}
print OUTLOG join "", (join "\t", ($tssClusterID, $chrom, $num_paraclu_cluster, $size, $num_read, $summit_pos, $summit_read, $num_sample_expr_cluster, $num_sample_expr_summit, $stability)), "\n";
print OUTBED $_."\n";
}
close FILEIN;
close OUTBED;
close OUTLOG;
&reportAndLogStatus("The final set contains $total_num clusters", 10, "\n");#->962
foreach my $param (sort keys %{$count_hsh_ref}) {
foreach my $cutoff (sort {$a <=> $b} keys %{$count_hsh_ref->{$param}}) {
my $count = $count_hsh_ref->{$param}{$cutoff};
my $pct = sprintf "%.2f", 100*$count/$total_num;
&reportAndLogStatus("With $param $cutoff n=$count [$pct%]", 10, "\n");#->962
}
}
return ();
}
sub printOutputFileListAndReadme {
#....................................................................................................................................................#
# subroutineCategory: output
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 3_finishingTasks|165
# secondaryAppearInSection: >none
# input: $ARGVStr, $outDir, $paramTag
# output:
# toCall: &printOutputFileListAndReadme($ARGVStr, $paramTag, $outDir);
# calledInLine: 168
#....................................................................................................................................................#
my ($ARGVStr, $paramTag, $outDir) = @_;
my $outputFileListPath = "$outDir/$paramTag/output.file.list.txt";
open (OUTFILELIST, ">", $outputFileListPath);
my %dirHsh = ();
my %filelistLenCountHsh = ();
push @{$filelistLenCountHsh{'dir'}}, length 'Directory';
push @{$filelistLenCountHsh{'name'}}, length 'Name';
push @{$filelistLenCountHsh{'description'}}, length 'Description';
foreach my $outputFilePath (sort {$a cmp $b} keys %{$globalReadmeHsh_ref}) {
my $fileDescription = $globalReadmeHsh_ref->{$outputFilePath}{'description'};
my $cleandOutputFilePath = $outputFilePath;
$cleandOutputFilePath =~ s/\/+/\//g;
my ($filePrefix, $fileDir, $fileSuffix) = fileparse($cleandOutputFilePath, qr/\.[^.]*/);
$fileDir =~ s/^$outDir//;
my $fileName = $filePrefix.$fileSuffix;
$dirHsh{$fileDir}{$fileName} = $fileDescription;
push @{$filelistLenCountHsh{'dir'}}, length $fileDir;
push @{$filelistLenCountHsh{'name'}}, length $fileName;
push @{$filelistLenCountHsh{'description'}}, length $fileDescription;
open README, ">", "$outputFilePath.readme.txt";
print README "=================\n";
print README "File descriptions\n";
print README "=================\n";
print README "$fileDescription\n";
if (exists $globalReadmeHsh_ref->{$outputFilePath}{'headerAry'}) {
my @colLenCountHsh = (length 'column');
push @colLenCountHsh, length $_ foreach (@{$globalReadmeHsh_ref->{$outputFilePath}{'headerAry'}});
my $headerColLen = max(@colLenCountHsh)+2;
print README "\n";
print README "\n";
print README "===================\n";
print README "Column descriptions\n";
print README "===================\n";
print README "\n";
printf README "%-".$headerColLen."s", 'column';
print README "description\n";
printf README "%-".$headerColLen."s", '------';
print README "-----------\n";
foreach my $header (@{$globalReadmeHsh_ref->{$outputFilePath}{'headerAry'}}) {
my $columnDescription = 'self-explanatory';
$columnDescription = $globalReadmeHsh_ref->{$outputFilePath}{'header'}{$header} if exists $globalReadmeHsh_ref->{$outputFilePath}{'header'}{$header};
printf README "%-".$headerColLen."s", $header;
print README $columnDescription."\n";
}
}
if (exists $globalReadmeHsh_ref->{$outputFilePath}{'extra_info'}) {
print README "\n";
print README "\n";
print README "=================\n";
print README "Extra information\n";
print README "=================\n";
print README "\n";
foreach my $title (sort keys %{$globalReadmeHsh_ref->{$outputFilePath}{'extra_info'}}) {
print README "$title\n";
print README "-" foreach (1..length $title);
print README "\n";
print README "$_\n" foreach @{$globalReadmeHsh_ref->{$outputFilePath}{'extra_info'}{$title}};
}
}
print README "\n";
print README "\n";
print README "~" foreach (1..length "$fileName was created from running,");
print README "\n";
print README "$fileName was created from running,\n";
print README "\n";
print README "$ARGVStr\n";
print README "\n";
close README;
}
my $fileDir_colLen = max(@{$filelistLenCountHsh{'dir'}})+2;
my $fileName_colLen = max(@{$filelistLenCountHsh{'name'}})+2;
my $fileDescription_colLen = max(@{$filelistLenCountHsh{'description'}})+2;
printf OUTFILELIST ("%-".$fileDir_colLen."s %-".$fileName_colLen."s %-".$fileDescription_colLen."s\n", 'directory', 'name', 'description');
printf OUTFILELIST ("%-".$fileDir_colLen."s %-".$fileName_colLen."s %-".$fileDescription_colLen."s\n", '=========', '====', '===========');
foreach my $fileDir (sort {$a cmp $b} keys %dirHsh) {
foreach my $fileName (sort {$a cmp $b} keys %{$dirHsh{$fileDir}}) {
my $fileDescription = $dirHsh{$fileDir}{$fileName};
printf OUTFILELIST ("%-".$fileDir_colLen."s %-".$fileName_colLen."s %-".$fileDescription_colLen."s\n", $fileDir, $fileName, $fileDescription);
}
}
print OUTFILELIST "\n";
print OUTFILELIST "\n";
print OUTFILELIST "~" foreach (1..length "The above files were generated by running,");
print OUTFILELIST "\n";
print OUTFILELIST "The above files were generated by running,\n";
print OUTFILELIST "\n";
print OUTFILELIST "$ARGVStr\n";
print OUTFILELIST "\n";
close OUTFILELIST;
return ();
}
sub printStartOrFinishMessage {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: currentTime|301
# appearInSub: >none
# primaryAppearInSection: 1_defineHardCodedParam|127, 3_finishingTasks|165
# secondaryAppearInSection: >none
# input: $StartOrFinishMessage
# output: none
# toCall: &printStartOrFinishMessage($StartOrFinishMessage);
# calledInLine: 144, 169
#....................................................................................................................................................#
my ($StartOrFinishMessage) = @_;
if ($StartOrFinishMessage eq "startMessage") {
print "\n=========================================================================\n";
print "[".¤tTime()."] starts running ...... \n";#->301
print "=========================================================================\n\n";
print $tmplog_fh "\n=========================================================================\n";
print $tmplog_fh "[".¤tTime()."] starts running ...... \n";#->301
print $tmplog_fh "=========================================================================\n\n";
} elsif ($StartOrFinishMessage eq "finishMessage") {
print "\n=========================================================================\n";
print "[".¤tTime()."] finished running .......\n";#->301
print "=========================================================================\n\n";
print $tmplog_fh "\n=========================================================================\n";
print $tmplog_fh "[".¤tTime()."] finished running .......\n";#->301
print $tmplog_fh "=========================================================================\n\n";
}
}
sub readParameters {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 0_startingTasks|119
# secondaryAppearInSection: >none
# input: none
# output: $cluster_ctss_bed_path, $count_ctss_bed_path_list, $count_scope_bed_path, $merge_dist, $min_cluster_count, $min_cluster_cpm, $min_num_sample_expr_cluster, $min_num_sample_expr_summit, $min_pos_count, $min_summit_count, $outDir, $outputPrefix, $overwrite
# toCall: my ($cluster_ctss_bed_path, $count_ctss_bed_path_list, $count_scope_bed_path, $min_cluster_cpm, $min_cluster_count, $min_pos_count, $min_summit_count, $merge_dist, $min_num_sample_expr_cluster, $min_num_sample_expr_summit, $outputPrefix, $outDir, $overwrite) = &readParameters();
# calledInLine: 122
#....................................................................................................................................................#
my ($cluster_ctss_bed_path, $count_ctss_bed_path_list, $count_scope_bed_path, $min_cluster_cpm, $min_cluster_count, $min_pos_count, $min_summit_count, $merge_dist, $min_num_sample_expr_cluster, $min_num_sample_expr_summit, $outputPrefix, $outDir, $overwrite);
$min_cluster_cpm = 1e-5;
$min_pos_count = 1;
$min_summit_count = 3;
$min_num_sample_expr_cluster = 5;
$min_num_sample_expr_summit = 3;
$min_cluster_count = 5;
$merge_dist = -1;
$overwrite= 'no';
GetOptions (
"cluster_ctss_bed_path=s" => \$cluster_ctss_bed_path,
"count_ctss_bed_path_list:s" => \$count_ctss_bed_path_list,
"count_scope_bed_path:s" => \$count_scope_bed_path,
"min_pos_count=i" => \$min_pos_count,
"min_cluster_cpm=f" => \$min_cluster_cpm,
"min_summit_count=s" => \$min_summit_count,
"min_cluster_count=s" => \$min_cluster_count,
"min_num_sample_expr_cluster=i" => \$min_num_sample_expr_cluster,
"min_num_sample_expr_summit=i" => \$min_num_sample_expr_summit,
"merge_dist=i" => \$merge_dist,
"outputPrefix=s" => \$outputPrefix,
"outDir=s" => \$outDir,
"overwrite=s" => \$overwrite,
'help' => sub { HelpMessage(0) },
) or HelpMessage(1);
HelpMessage(1) unless $cluster_ctss_bed_path;
#---check file
my $file_check_hsh_ref = {
'cluster_ctss_bed_path' => $cluster_ctss_bed_path,
};
foreach my $option_name (keys %{$file_check_hsh_ref}) {
my $file_path = $file_check_hsh_ref->{$option_name};
die "Quitting: File $option_name does not exists at $file_path" if not -s $file_path;
}
$count_ctss_bed_path_list = $cluster_ctss_bed_path if not defined $count_ctss_bed_path_list;
$count_scope_bed_path = $cluster_ctss_bed_path if not defined $count_scope_bed_path;
chop $outDir if ($outDir =~ m/\/$/); #---remove the last slash
system "mkdir -p -m 755 $outDir/";