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scafe.tool.cm.aggregate
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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 threads ('stack_size' => 64*4096);
use threads::shared;
use List::Util qw (sum shuffle min max);
use Cwd 'abs_path';
use AutoLoader qw/AUTOLOAD/;
#<\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.aggregate <---
<--- tool, common mode, aggregate ctss of multiple samples --->
Description:
This tool aggregate multiple ctss bed files, regardless of single cell or bulk
Usage:
scafe.tool.cm.aggregate [options] --lib_list_path --genome --outputPrefix --outDir
--lib_list_path <required> [string] a list of libraries, in formation of
<lib_ID><\t><collapse_ctss><\t><unencoded_G_collapse_ctss>
lib_ID = Unique ID of the lib
collapse_ctss = *.collapse.ctss.bed.gz from scafe.tool.sc.bam_to_ctss or scafe.tool.bk.bam_to_ctss
or *.pass.ctss.bed.gz from scafe.tool.cm.remove_strand_invader
unencoded_G_collapse_ctss = *unencoded_G.collapse.ctss.bed.gz from
scafe.tool.sc.bam_to_ctss or scafe.tool.bk.bam_to_ctss
--genome <required> [string] name of genome reference, e.g. hg19.gencode_v32lift37
--outputPrefix <required> [string] prefix for the output files
--outDir <required> [string] directory for the output files
--max_thread (optional) [integer] maximum number of parallel threads, capped at 10 to
avoid memory overflow (default=5)
--overwrite (optional) [yes/no] erase outDir/outputPrefix before running (default=no)
Dependencies:
bedtools
tabix
bgzip
For demo, cd to SCAFE dir and run,
scafe.tool.cm.aggregate \
--overwrite=yes \
--lib_list_path=./demo/input/cm.aggregate/lib_list_path.txt \
--genome=hg19.gencode_v32lift37 \
--outputPrefix=demo \
--outDir=./demo/output/cm.aggregate/aggregate/
=head1 VERSION
v0.9.0-beta [March 20, 2021]
-Exists as scafe.tool.sc.pool/scafe.tool.bk.pool
v1.0.0 [June 6, 2022]
-Initial release
=cut
#<\doc>
#====================================================================================================================================================#
#====================================================================================================================================================#
#<lastCmdCalled>
#
# notCalledBefore
#
# notCalledBefore
#
#<\lastCmdCalled>
#====================================================================================================================================================#
#====================================================================================================================================================#
#<global>
my $scriptDirPath = dirname(rel2abs($0));
my $scriptAbsPath = abs_path($0);
my ($curntTimeStamp) = &timeStamp();#->974
my $ARGVStr = join "\n", (¤tTime(), $scriptAbsPath, @ARGV);#->420
my $globalReadmeHsh_ref = {};
our $tmplog_fh;
#<\global>
#====================================================================================================================================================#
#====================================================================================================================================================#
{ #Main sections lexical scope starts
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 0_startingTasks
#
#<section ID="startingTasks" num="0">
my ($lib_list_path, $max_thread, $genome, $outputPrefix, $outDir, $overwrite) = &readParameters();#->906
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 1_defineHardCodedParam
#
#<section ID="defineHardCodedParam" num="1">
my $paramTag = "$outputPrefix";
my $num_chunk = 100;
my $bgzip_sort_thread = 5;
$max_thread = 10 if $max_thread > 10;
my $rm_tmp_file = 'yes';
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 2_defineOutDirPath
#
#<section ID="defineOutDirPath" num="2">
my @mkDirAry;
my $result_dir = "$outDir/$paramTag"; push @mkDirAry, $result_dir;
system "rm -rf $result_dir" if ($overwrite eq 'yes');
my $result_bed_dir = "$result_dir/bed/"; push @mkDirAry, $result_bed_dir;
my $result_log_dir = "$result_dir/log/"; push @mkDirAry, $result_log_dir;
my $result_tmp_dir = "$result_dir/tmp/"; push @mkDirAry, $result_tmp_dir;
my $result_script_dir = "$result_dir/script/"; push @mkDirAry, $result_script_dir;
foreach my $dir (@mkDirAry) {system ("mkdir -pm 755 $dir");}
open $tmplog_fh, ">", "$result_dir/00_screen_log.$curntTimeStamp.log.txt";
&logCalledCMDAndScript($ARGVStr, $result_script_dir, $scriptAbsPath);#->536
&printStartOrFinishMessage("startMessage");#->767
my ($tabix_bin, $bgzip_bin, $bedtools_bin, $samtools_bin, $paraclu_bin, $cut_sh_path, $bedGraphToBigWig_bin, $bigWigAverageOverBed_bin) = &checkAllExecutable();#->203
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 3_generate_chunk
#
#<section ID="generate_chunk" num="3">
my ($chrom_size_path) = &checkChromSizePath($genome);#->303
my ($chrom_size_hsh_ref) = &generateChromSizeHsh($chrom_size_path);#->438
my ($chunk_size) = &generateChunkSize($chrom_size_hsh_ref, $num_chunk);#->511
my ($chunk_info_hsh_ref) = &generateChunkInfoHsh($chrom_size_hsh_ref, $chunk_size, $result_tmp_dir);#->464
my ($lib_info_hsh_ref) = &readLibInfo($lib_list_path);#->881
($lib_info_hsh_ref) = &checkTabixBgzipCtss($tabix_bin, $bgzip_bin, $lib_info_hsh_ref, $max_thread, $result_tmp_dir, $bgzip_sort_thread);#->346
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 4_convert
#
#<section ID="convert" num="4">
&processPerChunk($lib_info_hsh_ref, $bedtools_bin, $max_thread, $chunk_info_hsh_ref, $bgzip_sort_thread, $tabix_bin, $bgzip_bin);#->801
&poolChunkResults($chunk_info_hsh_ref, $result_bed_dir, $result_log_dir, $paramTag, $result_tmp_dir, $rm_tmp_file, $tabix_bin);#->561
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 5_finishingTasks
#
#<section ID="finishingTasks" num="5">
&printOutputFileListAndReadme($ARGVStr, $paramTag, $outDir);#->652
&printStartOrFinishMessage("finishMessage");#->767
#<\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=11]:
# checkAllExecutable, checkChromSizePath, checkChunkResults
# checkTabixBgzipCtss, generateChromSizeHsh, generateChunkInfoHsh
# generateChunkSize, poolChunkResults, poolLibCTSSPerChunk
# processPerChunk, readLibInfo
#
#====================================================================================================================================================#
sub checkAllExecutable {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|952
# appearInSub: >none
# primaryAppearInSection: 2_defineOutDirPath|125
# 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: 139
#....................................................................................................................................................#
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");#->952
{
my $stdOut = `$tabix_bin --version 2>&1`;
if ($stdOut =~ m/tabix \(htslib\) (\S+)/) {
&reportAndLogStatus("Checking: tabix version: $1", 0, "\n");#->952
} 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");#->952
} 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");#->952
} 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");#->952
} 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");#->952
} 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");#->952
} 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");#->952
} else {
die "bedGraphToBigWig not installed properly. Quitting.\n";
}
}
{
my $stdOut = `$bigWigAverageOverBed_bin 2>&1`;
if ($stdOut =~ m/bigWigAverageOverBed v(\S+)/) {
&reportAndLogStatus("Checking: bigWigAverageOverBed version: $1", 0, "\n");#->952
} else {
die "bigWigAverageOverBed is not installed properly. Quitting.\n";
}
}
return ($tabix_bin, $bgzip_bin, $bedtools_bin, $samtools_bin, $paraclu_bin, $cut_sh_path, $bedGraphToBigWig_bin, $bigWigAverageOverBed_bin);
}
sub checkChromSizePath {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 3_generate_chunk|144
# secondaryAppearInSection: >none
# input: $genome
# output: $chrom_size_path
# toCall: my ($chrom_size_path) = &checkChromSizePath($genome);
# calledInLine: 147
#....................................................................................................................................................#
my ($genome) = @_;
my $dirPath = dirname(rel2abs($0));
my $chrom_size_path = "$dirPath/../resources/genome/$genome/tsv/chrom.sizes.tsv";
die "genome $genome does not have chrom_size_path. Please rerun prep_genome step\n" if not -s $chrom_size_path;
return ($chrom_size_path);
}
sub checkChunkResults {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|952
# appearInSub: poolChunkResults|561, processPerChunk|801
# primaryAppearInSection: >none
# secondaryAppearInSection: 4_convert|157
# input: $chunk_info_hsh_ref, $chunk_num, $file_check_ary_ref
# output: $valid
# toCall: my ($valid) = &checkChunkResults($chunk_info_hsh_ref, $chunk_num, $file_check_ary_ref);
# calledInLine: 584, 839
#....................................................................................................................................................#
my ($chunk_info_hsh_ref, $chunk_num, $file_check_ary_ref) = @_;
my $valid = 'yes';
foreach my $file_to_check (@{$file_check_ary_ref}) {
my $file_path = $chunk_info_hsh_ref->{$chunk_num}{'ctss'}{'sorted'}{$file_to_check};
#&reportAndLogStatus("$file_path", 10, "\n");#->952
$valid = 'no' if not -f $file_path;
}
return ($valid);
}
sub checkTabixBgzipCtss {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|952
# appearInSub: >none
# primaryAppearInSection: 3_generate_chunk|144
# secondaryAppearInSection: >none
# input: $bgzip_bin, $bgzip_sort_thread, $lib_info_hsh_ref, $max_thread, $result_tmp_dir, $tabix_bin
# output: $lib_info_hsh_ref
# toCall: my ($lib_info_hsh_ref) = &checkTabixBgzipCtss($tabix_bin, $bgzip_bin, $lib_info_hsh_ref, $max_thread, $result_tmp_dir, $bgzip_sort_thread);
# calledInLine: 152
#....................................................................................................................................................#
my ($tabix_bin, $bgzip_bin, $lib_info_hsh_ref, $max_thread, $result_tmp_dir, $bgzip_sort_thread) = @_;
my %itemForThrHsh = ();
my $threadID = 1;
foreach my $libID (shuffle(keys %{$lib_info_hsh_ref})) {
$threadID = 1 if $threadID > $max_thread;
push @{$itemForThrHsh{$threadID}} , $libID;
$threadID++;
}
my %threadHsh =();
foreach my $threadID (sort keys %itemForThrHsh) {
my $itemForThrAry_ref = $itemForThrHsh{$threadID};
($threadHsh{$threadID}) = threads->new(#---refer to http://www.perlmonks.org/?node_id=966781, the
sub {
my ($itemForThrAry_ref) = @_;
my $lib_info_inThr_hsh_ref = {};
foreach my $libID (@{$itemForThrAry_ref}) {
#---[2/19/16 13:13] do something on the item here
foreach my $ctss_type (qw/unencoded_G_collapse_ctss collapse_ctss/) {
my $original_ctss_path = $lib_info_hsh_ref->{$libID}{$ctss_type};
my $check_original_index = `$tabix_bin -l $original_ctss_path 2>&1`;
#&reportAndLogStatus("$check_original_index", 10, "\n");#->952
my $tabix_ctss_path = $original_ctss_path;
if ($check_original_index =~ m/Could not load .tbi index/) {
$tabix_ctss_path = "$result_tmp_dir/$libID.$ctss_type.bed.gz";
&reportAndLogStatus("Creating tabix index of $ctss_type in $libID", 10, "\n");#->952
system "$bgzip_bin -@ $bgzip_sort_thread -dc $original_ctss_path | $bgzip_bin -@ $bgzip_sort_thread -c >$tabix_ctss_path";
system "$tabix_bin -p bed $tabix_ctss_path";
} else {
&reportAndLogStatus("Tabix index found for $ctss_type in $libID", 10, "\n");#->952
}
my $check_tabix_index = `$tabix_bin -l $tabix_ctss_path 2>&1`;
die "Tabix index failed for for $ctss_type in $libID" if ($check_tabix_index =~ m/Could not load .tbi index/);
$lib_info_inThr_hsh_ref->{$libID}{'tabix_ctss_path'}{$ctss_type} = $tabix_ctss_path;
}
}
return ($lib_info_inThr_hsh_ref);
}
,($itemForThrAry_ref)
);
}
my $data_hsh_ref = {};
while (keys %threadHsh) {
foreach my $threadID (keys %threadHsh) {
if (not $threadHsh{$threadID}->is_running()) {
my ($lib_info_inThr_hsh_ref) = $threadHsh{$threadID}->join;
foreach my $libID (keys %{$lib_info_inThr_hsh_ref}) {
foreach my $ctss_type (keys %{$lib_info_inThr_hsh_ref->{$libID}{'tabix_ctss_path'}}) {
$lib_info_hsh_ref->{$libID}{'tabix_ctss_path'}{$ctss_type} = $lib_info_inThr_hsh_ref->{$libID}{'tabix_ctss_path'}{$ctss_type};
}
}
delete $threadHsh{$threadID};
}
}
sleep 1;
}
return ($lib_info_hsh_ref);
}
sub currentTime {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: >none
# appearInSub: printStartOrFinishMessage|767, reportAndLogStatus|952
# primaryAppearInSection: >none
# secondaryAppearInSection: 2_defineOutDirPath|125, 5_finishingTasks|166
# input: none
# output: $runTime
# toCall: my ($runTime) = ¤tTime();
# calledInLine: 94, 783, 787, 792, 796, 968, 969
#....................................................................................................................................................#
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 generateChromSizeHsh {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 3_generate_chunk|144
# secondaryAppearInSection: >none
# input: $chrom_size_path
# output: $chrom_size_hsh_ref
# toCall: my ($chrom_size_hsh_ref) = &generateChromSizeHsh($chrom_size_path);
# calledInLine: 148
#....................................................................................................................................................#
my ($chrom_size_path) = @_;
my $chrom_size_hsh_ref = {};
open (CHROMSIZE, "<", $chrom_size_path);
while (<CHROMSIZE>) {
chomp;
my ($chrom, $size) = split /\s+/;
$chrom_size_hsh_ref->{$chrom} = $size;
}
close CHROMSIZE;
return ($chrom_size_hsh_ref);
}
sub generateChunkInfoHsh {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|952
# appearInSub: >none
# primaryAppearInSection: 3_generate_chunk|144
# secondaryAppearInSection: >none
# input: $chrom_size_hsh_ref, $chunk_size, $result_tmp_dir
# output: $chunk_info_hsh_ref
# toCall: my ($chunk_info_hsh_ref) = &generateChunkInfoHsh($chrom_size_hsh_ref, $chunk_size, $result_tmp_dir);
# calledInLine: 150
#....................................................................................................................................................#
my ($chrom_size_hsh_ref, $chunk_size, $result_tmp_dir) = @_;
my $chunk_num = 1;
my $chunk_info_hsh_ref = {};
foreach my $chrom (sort {$a cmp $b} keys %{$chrom_size_hsh_ref}) {
my $size = $chrom_size_hsh_ref->{$chrom};
foreach (my $startPos = 0; $startPos <= $size; $startPos += $chunk_size) {
my $endPos = $startPos + $chunk_size ;
$endPos = $size if ($endPos > $size);
my $file_tag = "$chrom.$startPos.$endPos";
my $size_in_chunk = $endPos - $startPos;
&reportAndLogStatus("chunk $chunk_num contains $size_in_chunk nt covering $chrom $startPos to $endPos", 10, "\n");#->952
my $chunk_sorted_unencoded_G_collapse_ctss = "$result_tmp_dir/$file_tag.sorted.merged.unencoded_G_collapsed.ctss.bed.gz";
my $chunk_sorted_collapse_ctss = "$result_tmp_dir/$file_tag.sorted.merged.strand_invader_removed.ctss.bed.gz";
my $chunk_unsort_unencoded_G_collapse_ctss = "$result_tmp_dir/$file_tag.unsorted.unencoded_G_collapsed.ctss.bed";
my $chunk_unsort_collapse_ctss = "$result_tmp_dir/$file_tag.unsorted.strand_invader_removed.ctss.bed";
my ($chunk_chrom, $chunk_startPos, $chunk_endPos) = ($chrom, $startPos, $endPos);
my $tabix_startPos = $chunk_startPos + 1; #---[2021/09/01 22:58] everything is zero based except tabix
$chunk_info_hsh_ref->{$chunk_num}{'file_tag'} = $file_tag;
$chunk_info_hsh_ref->{$chunk_num}{'loc'} = [$chunk_chrom, $chunk_startPos, $chunk_endPos];
$chunk_info_hsh_ref->{$chunk_num}{'region_str'} = "$chunk_chrom:$chunk_startPos-$chunk_endPos";
$chunk_info_hsh_ref->{$chunk_num}{'tabix_region_str'} = "$chunk_chrom:$tabix_startPos-$chunk_endPos";
$chunk_info_hsh_ref->{$chunk_num}{'ctss'}{'unsort'}{'collapse_ctss'} = $chunk_unsort_collapse_ctss;
$chunk_info_hsh_ref->{$chunk_num}{'ctss'}{'unsort'}{'unencoded_G_collapse_ctss'} = $chunk_unsort_unencoded_G_collapse_ctss;
$chunk_info_hsh_ref->{$chunk_num}{'ctss'}{'sorted'}{'collapse_ctss'} = $chunk_sorted_collapse_ctss;
$chunk_info_hsh_ref->{$chunk_num}{'ctss'}{'sorted'}{'unencoded_G_collapse_ctss'} = $chunk_sorted_unencoded_G_collapse_ctss;
$chunk_num++;
}
}
return ($chunk_info_hsh_ref);
}
sub generateChunkSize {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 3_generate_chunk|144
# secondaryAppearInSection: >none
# input: $chrom_size_hsh_ref, $num_chunk
# output: $chunk_size
# toCall: my ($chunk_size) = &generateChunkSize($chrom_size_hsh_ref, $num_chunk);
# calledInLine: 149
#....................................................................................................................................................#
my ($chrom_size_hsh_ref, $num_chunk) = @_;
my $total_size = 0;
foreach my $chrom (keys %{$chrom_size_hsh_ref}) {
$total_size += $chrom_size_hsh_ref->{$chrom};
}
my $chunk_size = int ($total_size/$num_chunk);
return ($chunk_size);
}
sub logCalledCMDAndScript {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 2_defineOutDirPath|125
# secondaryAppearInSection: >none
# input: $ARGVStr, $result_script_dir, $scriptAbsPath
# output:
# toCall: &logCalledCMDAndScript($ARGVStr, $result_script_dir, $scriptAbsPath);
# calledInLine: 137
#....................................................................................................................................................#
my ($ARGVStr, $result_script_dir, $scriptAbsPath) = @_;
my $cpScriptPath = "$result_script_dir/script.ran.pl";
my $calledCMDPath = "$result_script_dir/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 poolChunkResults {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: checkChunkResults|323, reportAndLogStatus|952
# appearInSub: >none
# primaryAppearInSection: 4_convert|157
# secondaryAppearInSection: >none
# input: $chunk_info_hsh_ref, $paramTag, $result_bed_dir, $result_log_dir, $result_tmp_dir, $rm_tmp_file, $tabix_bin
# output:
# toCall: &poolChunkResults($chunk_info_hsh_ref, $result_bed_dir, $result_log_dir, $paramTag, $result_tmp_dir, $rm_tmp_file, $tabix_bin);
# calledInLine: 161
#....................................................................................................................................................#
my ($chunk_info_hsh_ref, $result_bed_dir, $result_log_dir, $paramTag, $result_tmp_dir, $rm_tmp_file, $tabix_bin) = @_;
my $out_bed_hsh_ref = {
'collapse_ctss' => "$result_bed_dir/$paramTag.aggregate.collapse.ctss.bed.gz",
'unencoded_G_collapse_ctss' => "$result_bed_dir/$paramTag.aggregate.unencoded_G.collapse.ctss.bed.gz",
};
foreach my $ctss_type (keys %{$out_bed_hsh_ref}) {
my $out_ctss_type = $out_bed_hsh_ref->{$ctss_type};
my @file_path_ary = ();
foreach my $chunk_num (sort {$a <=> $b} keys %{$chunk_info_hsh_ref}) {
my $file_check_ary_ref = [$ctss_type];
my ($valid) = &checkChunkResults($chunk_info_hsh_ref, $chunk_num, $file_check_ary_ref);#->323
if ($valid eq 'yes') {
my $chunk_sorted_ctss = $chunk_info_hsh_ref->{$chunk_num}{'ctss'}{'sorted'}{$ctss_type};
push @file_path_ary, $chunk_sorted_ctss;
&reportAndLogStatus("$ctss_type of chunk $chunk_num is found", 10, "\n");#->952
} else {
die "results of chunk $chunk_num is not found. quitting\n";
}
}
&reportAndLogStatus("Concatenating $ctss_type files", 10, "\n");#->952
my $file_path_str = join " ", @file_path_ary;
system "cat $file_path_str >$out_ctss_type";
&reportAndLogStatus("Tabix indexing combined $ctss_type", 10, "\n");#->952
system "$tabix_bin -p bed $out_ctss_type";
}
if ($rm_tmp_file eq 'yes') {
&reportAndLogStatus("Removing result_tmp_dir", 10, "\n");#->952
system "rm -rf $result_tmp_dir";
}
return ();
}
sub poolLibCTSSPerChunk {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|952
# appearInSub: processPerChunk|801
# primaryAppearInSection: >none
# secondaryAppearInSection: 4_convert|157
# input: $bedtools_bin, $bgzip_bin, $bgzip_sort_thread, $chunk_info_hsh_ref, $chunk_num, $lib_info_hsh_ref, $tabix_bin
# output:
# toCall: &poolLibCTSSPerChunk($lib_info_hsh_ref, $chunk_info_hsh_ref, $chunk_num, $bgzip_sort_thread, $tabix_bin, $bedtools_bin, $bgzip_bin);
# calledInLine: 846
#....................................................................................................................................................#
my ($lib_info_hsh_ref, $chunk_info_hsh_ref, $chunk_num, $bgzip_sort_thread, $tabix_bin, $bedtools_bin, $bgzip_bin) = @_;
my $tabix_region_str = $chunk_info_hsh_ref->{$chunk_num}{'tabix_region_str'};
#---[2021/08/22 14:45] tabix_region_str has a 1 based start position to prevent overlapping of the chunk junction
foreach my $ctss_type (qw/collapse_ctss unencoded_G_collapse_ctss/) {
my $chunk_unsort_ctss = $chunk_info_hsh_ref->{$chunk_num}{'ctss'}{'unsort'}{$ctss_type};
my $chunk_sorted_ctss = $chunk_info_hsh_ref->{$chunk_num}{'ctss'}{'sorted'}{$ctss_type};
my $num_read = 0;
open UNSORT, ">$chunk_unsort_ctss";
foreach my $libID (keys %{$lib_info_hsh_ref}) {
&reportAndLogStatus("pooling $libID in chunk $chunk_num $ctss_type", 10, "\n");#->952
my $tabix_ctss_path = $lib_info_hsh_ref->{$libID}{'tabix_ctss_path'}{$ctss_type};
open (TABIX, "$tabix_bin $tabix_ctss_path $tabix_region_str |");
while (<TABIX>) {
print UNSORT $_;
$num_read++;
}
close TABIX;
}
close UNSORT;
&reportAndLogStatus("sorting and merging $ctss_type in chunk $chunk_num.", 10, "\n");#->952
if ($num_read > 0) {
system "sort --parallel $bgzip_sort_thread -k2,2n -k6,6 $chunk_unsort_ctss | $bedtools_bin merge -d -1 -s -c 4,5,6 -o sum,sum,distinct | $bgzip_bin -@ $bgzip_sort_thread >$chunk_sorted_ctss";
} else {
system "$bgzip_bin < /dev/null >$chunk_sorted_ctss";
}
system "rm $chunk_unsort_ctss";
}
return ();
}
sub printOutputFileListAndReadme {
#....................................................................................................................................................#
# subroutineCategory: output
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 5_finishingTasks|166
# secondaryAppearInSection: >none
# input: $ARGVStr, $outDir, $paramTag
# output:
# toCall: &printOutputFileListAndReadme($ARGVStr, $paramTag, $outDir);
# calledInLine: 169
#....................................................................................................................................................#
my ($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|420
# appearInSub: >none
# primaryAppearInSection: 2_defineOutDirPath|125, 5_finishingTasks|166
# secondaryAppearInSection: >none
# input: $StartOrFinishMessage
# output: none
# toCall: &printStartOrFinishMessage($StartOrFinishMessage);
# calledInLine: 138, 170
#....................................................................................................................................................#
my ($StartOrFinishMessage) = @_;
if ($StartOrFinishMessage eq "startMessage") {
print "\n=========================================================================\n";
print "[".¤tTime()."] starts running ...... \n";#->420
print "=========================================================================\n\n";
print $tmplog_fh "\n=========================================================================\n";
print $tmplog_fh "[".¤tTime()."] starts running ...... \n";#->420
print $tmplog_fh "=========================================================================\n\n";
} elsif ($StartOrFinishMessage eq "finishMessage") {
print "\n=========================================================================\n";
print "[".¤tTime()."] finished running .......\n";#->420
print "=========================================================================\n\n";
print $tmplog_fh "\n=========================================================================\n";
print $tmplog_fh "[".¤tTime()."] finished running .......\n";#->420
print $tmplog_fh "=========================================================================\n\n";
}
}
sub processPerChunk {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: checkChunkResults|323, poolLibCTSSPerChunk|608, reportAndLogStatus|952
# appearInSub: >none
# primaryAppearInSection: 4_convert|157
# secondaryAppearInSection: >none
# input: $bedtools_bin, $bgzip_bin, $bgzip_sort_thread, $chunk_info_hsh_ref, $lib_info_hsh_ref, $max_thread, $tabix_bin
# output:
# toCall: &processPerChunk($lib_info_hsh_ref, $bedtools_bin, $max_thread, $chunk_info_hsh_ref, $bgzip_sort_thread, $tabix_bin, $bgzip_bin);
# calledInLine: 160
#....................................................................................................................................................#
my ($lib_info_hsh_ref, $bedtools_bin, $max_thread, $chunk_info_hsh_ref, $bgzip_sort_thread, $tabix_bin, $bgzip_bin) = @_;
my %itemForThrHsh = ();
my $threadID = 1;
my $chrom_info_hsh_ref = {};
my $total_num_chunk = keys %{$chunk_info_hsh_ref};
foreach my $chunk_num (keys %{$chunk_info_hsh_ref}) {
$threadID = 1 if $threadID > $max_thread;
$itemForThrHsh{$threadID}{$chunk_num}++;
$threadID++;
}
my $num_proc : shared = 0;
my %threadHsh =();
foreach my $threadID (sort {$a <=> $b} keys %itemForThrHsh) {
my $itemForThrHsh_ref = $itemForThrHsh{$threadID};
($threadHsh{$threadID}) = threads->new(#---refer to http://www.perlmonks.org/?node_id=966781, the
sub {
my ($itemForThrHsh_ref) = @_;
my $total_chunk = keys %{$itemForThrHsh_ref};
&reportAndLogStatus("$total_chunk chunks spawned to thread $threadID.", 10, "\n");#->952
foreach my $chunk_num (keys %{$itemForThrHsh_ref}) {
my $file_check_ary_ref = [qw/unencoded_G_collapse_ctss collapse_ctss/];
my ($valid) = &checkChunkResults($chunk_info_hsh_ref, $chunk_num, $file_check_ary_ref);#->323
if ($valid eq 'yes') {
&reportAndLogStatus("results of chunk $chunk_num is found. skipping", 10, "\n");#->952
} else {
&reportAndLogStatus("start processing chunk $chunk_num in thread $threadID.", 10, "\n");#->952
&poolLibCTSSPerChunk($lib_info_hsh_ref, $chunk_info_hsh_ref, $chunk_num, $bgzip_sort_thread, $tabix_bin, $bedtools_bin, $bgzip_bin);#->608
}
$num_proc++;
&reportAndLogStatus("$num_proc of $total_num_chunk chunks are finised.", 10, "\n");#->952
}
return ();
}
,($itemForThrHsh_ref)
);
}
while (keys %threadHsh) {
my @threads = threads->list();
my $thread_count = threads->list();
my @running = threads->list(threads::running);
my @joinable = threads->list(threads::joinable);
my $running_count = @running;
my $joinable_count = @joinable;
&reportAndLogStatus("$thread_count threads exists. $running_count running and $joinable_count joinable", 10, "\n");#->952
foreach my $threadID (keys %threadHsh) {
if (not $threadHsh{$threadID}->is_running() or $threadHsh{$threadID}->is_joinable() or $threadHsh{$threadID}->is_detached()) {
&reportAndLogStatus("thread $threadID is finishing.", 10, "\n");#->952
$threadHsh{$threadID}->join();
delete $threadHsh{$threadID};
}
}
sleep 10;
}
return ();
}
sub readLibInfo {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 3_generate_chunk|144
# secondaryAppearInSection: >none
# input: $lib_list_path
# output: $lib_info_hsh_ref
# toCall: my ($lib_info_hsh_ref) = &readLibInfo($lib_list_path);
# calledInLine: 151
#....................................................................................................................................................#
my ($lib_list_path) = @_;
my $lib_info_hsh_ref = {};
open LIBINFO, "<", $lib_list_path;
while (<LIBINFO>) {
chomp;
my ($libID, $collapse_ctss, $unencoded_G_collapse_ctss) = split /\t/;
$lib_info_hsh_ref->{$libID}{'collapse_ctss'} = $collapse_ctss;
$lib_info_hsh_ref->{$libID}{'unencoded_G_collapse_ctss'} = $unencoded_G_collapse_ctss;
}
return ($lib_info_hsh_ref);
}
sub readParameters {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 0_startingTasks|105
# secondaryAppearInSection: >none
# input: none
# output: $genome, $lib_list_path, $max_thread, $outDir, $outputPrefix, $overwrite
# toCall: my ($lib_list_path, $max_thread, $genome, $outputPrefix, $outDir, $overwrite) = &readParameters();
# calledInLine: 108
#....................................................................................................................................................#
my ($lib_list_path, $max_thread, $genome, $outputPrefix, $outDir, $overwrite);
$overwrite = 'no';
$max_thread = 5;
GetOptions (
"lib_list_path=s" => \$lib_list_path,
"max_thread:i" => \$max_thread,
"genome=s" => \$genome,
"outputPrefix=s" => \$outputPrefix,
"outDir:s" => \$outDir,
"overwrite:s" => \$overwrite,
'help' => sub { HelpMessage(0) },
) or HelpMessage(1);
HelpMessage(1) unless $lib_list_path;
#---check file
my $file_check_hsh_ref = {
'lib_list_path' => $lib_list_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;
}
chop $outDir if ($outDir =~ m/\/$/); #---remove the last slash
system "mkdir -p -m 755 $outDir/";
return($lib_list_path, $max_thread, $genome, $outputPrefix, $outDir, $overwrite);
}