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scafe.tool.bk.subsample_ctss
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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>
#====================================================================================================================================================#
#====================================================================================================================================================#
#<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.bk.subsample_ctss <---
<--- tool, bulk mode, subsample ctss --->
Description:
This tool subsample a ctss bed file from bulk CAGE ctss
Usage:
scafe.tool.bk.subsample_ctss [options] --UMI_CB_ctss_bed_path --subsample_num --outputPrefix --outDir
--long_ctss_bed_path <required> [string] ctss file for subsampling, one line read in "long" format,
*long.ctss.bed.gz from scafe.tool.bk.bam_to_ctss.pl,
--subsample_num <required> [integer] number of UMI to be subsampled
--outputPrefix <required> [string] prefix for the output files
--outDir <required> [string] directory for the output files
--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.bk.subsample_ctss \
--overwrite=yes \
--long_ctss_bed_path=./demo/output/bk.solo/bam_to_ctss/demo/bed/demo.long.ctss.bed.gz \
--subsample_num=100000 \
--outputPrefix=demo \
--outDir=./demo/output/bk.subsample/subsample_ctss/
=head1 VERSION
v0.9.0-beta [March 20, 2021]
-Initial pre-release
v1.0.0 [June 6, 2022]
-use tabix and bgzip for ctss bed
=cut
#<\doc>
#====================================================================================================================================================#
#====================================================================================================================================================#
#<lastCmdCalled>
#
# notCalledBefore
#
# notCalledBefore
#
#<\lastCmdCalled>
#====================================================================================================================================================#
#====================================================================================================================================================#
#<global>
my $scriptDirPath = dirname(rel2abs($0));
my $scriptAbsPath = abs_path($0);
my ($curntTimeStamp) = &timeStamp();#->686
my $ARGVStr = join "\n", (¤tTime(), $scriptAbsPath, @ARGV);#->289
my $globalReadmeHsh_ref = {};
our $tmplog_fh;
#<\global>
#====================================================================================================================================================#
#====================================================================================================================================================#
{ #Main sections lexical scope starts
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 0_startingTasks
#
#<section ID="startingTasks" num="0">
my ($long_ctss_bed_path, $subsample_num, $outputPrefix, $outDir, $overwrite) = &readParameters();#->524
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 1_defineHardCodedParam
#
#<section ID="defineHardCodedParam" num="1">
my $paramTag = "$outputPrefix";
my $max_thread = 5;
#<\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 $result_script_dir = "$result_dir/script/"; push @mkDirAry, $result_script_dir;
foreach my $dir (@mkDirAry) {system ("mkdir -pm 777 $dir");}
open $tmplog_fh, ">", "$result_dir/00_screen_log.$curntTimeStamp.log.txt";
&logCalledCMDAndScript($ARGVStr, $result_script_dir, $scriptAbsPath);#->350
&printStartOrFinishMessage("startMessage");#->490
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 3_subsample
#
#<section ID="subsample" num="3">
my ($tabix_bin, $bgzip_bin, $bedtools_bin, $samtools_bin, $paraclu_bin, $cut_sh_path, $bedGraphToBigWig_bin, $bigWigAverageOverBed_bin) = &checkAllExecutable();#->189
my ($target_fraction) = &getTargetFraction($long_ctss_bed_path, $subsample_num);#->307
&subsampleCTSS($long_ctss_bed_path, $result_bed_dir, $bedtools_bin, $target_fraction, $tabix_bin, $bgzip_bin, $max_thread, $outputPrefix);#->590
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 4_convert
#
#<section ID="convert" num="4">
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 5_finishingTasks
#
#<section ID="finishingTasks" num="5">
&printOutputFileListAndReadme($ARGVStr, $paramTag, $outDir);#->375
&printStartOrFinishMessage("finishMessage");#->490
#<\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=3]:
# checkAllExecutable, getTargetFraction, subsampleCTSS
#
#====================================================================================================================================================#
sub checkAllExecutable {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|568
# appearInSub: >none
# primaryAppearInSection: 3_subsample|138
# 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: 141
#....................................................................................................................................................#
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");#->568
{
my $stdOut = `$tabix_bin --version 2>&1`;
if ($stdOut =~ m/tabix \(htslib\) (\S+)/) {
&reportAndLogStatus("Checking: tabix version: $1", 0, "\n");#->568
} 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");#->568
} 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");#->568
} 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");#->568
} 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");#->568
} 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");#->568
} 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");#->568
} else {
die "bedGraphToBigWig not installed properly. Quitting.\n";
}
}
{
my $stdOut = `$bigWigAverageOverBed_bin 2>&1`;
if ($stdOut =~ m/bigWigAverageOverBed v(\S+)/) {
&reportAndLogStatus("Checking: bigWigAverageOverBed version: $1", 0, "\n");#->568
} else {
die "bigWigAverageOverBed is not installed properly. Quitting.\n";
}
}
return ($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|490, reportAndLogStatus|568
# primaryAppearInSection: >none
# secondaryAppearInSection: 2_defineOutDirPath|121, 5_finishingTasks|155
# input: none
# output: $runTime
# toCall: my ($runTime) = ¤tTime();
# calledInLine: 94, 506, 510, 515, 519, 584, 585
#....................................................................................................................................................#
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 getTargetFraction {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|568
# appearInSub: >none
# primaryAppearInSection: 3_subsample|138
# secondaryAppearInSection: >none
# input: $long_ctss_bed_path, $subsample_num
# output: $target_fraction
# toCall: my ($target_fraction) = &getTargetFraction($long_ctss_bed_path, $subsample_num);
# calledInLine: 142
#....................................................................................................................................................#
my ($long_ctss_bed_path, $subsample_num) = @_;
&reportAndLogStatus("getting total num", 10, "\n");#->568
my $total_num = 0;
my $ung_num = 0;
if ($long_ctss_bed_path =~ m/\.gz$/) {
open (FILEIN, " gzip -dc $long_ctss_bed_path | cut -f 5 |");
} else {
open (FILEIN, "cut -f 5 $long_ctss_bed_path |");
}
while (<FILEIN>) {
chomp (my $ung = $_);
$total_num++;
$ung_num++ if $ung > 0;
}
close FILEIN;
my $target_fraction = $subsample_num/$total_num;
if ($target_fraction > 1) {
$target_fraction = 1;
&reportAndLogStatus("subsample_num is greater than total_num", 10, "\n");#->568
&reportAndLogStatus("limiting target_fraction to 1", 10, "\n");#->568
}
&reportAndLogStatus("total_num=$total_num", 10, "\n");#->568
&reportAndLogStatus("unencoded_G_num=$ung_num", 10, "\n");#->568
&reportAndLogStatus("subsample_num=$subsample_num", 10, "\n");#->568
&reportAndLogStatus("target_fraction=$target_fraction", 10, "\n");#->568
return ($target_fraction);
}
sub logCalledCMDAndScript {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 2_defineOutDirPath|121
# secondaryAppearInSection: >none
# input: $ARGVStr, $result_script_dir, $scriptAbsPath
# output:
# toCall: &logCalledCMDAndScript($ARGVStr, $result_script_dir, $scriptAbsPath);
# calledInLine: 132
#....................................................................................................................................................#
my ($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 printOutputFileListAndReadme {
#....................................................................................................................................................#
# subroutineCategory: output
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 5_finishingTasks|155
# secondaryAppearInSection: >none
# input: $ARGVStr, $outDir, $paramTag
# output:
# toCall: &printOutputFileListAndReadme($ARGVStr, $paramTag, $outDir);
# calledInLine: 158
#....................................................................................................................................................#
my ($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|289
# appearInSub: >none
# primaryAppearInSection: 2_defineOutDirPath|121, 5_finishingTasks|155
# secondaryAppearInSection: >none
# input: $StartOrFinishMessage
# output: none
# toCall: &printStartOrFinishMessage($StartOrFinishMessage);
# calledInLine: 133, 159
#....................................................................................................................................................#
my ($StartOrFinishMessage) = @_;
if ($StartOrFinishMessage eq "startMessage") {
print "\n=========================================================================\n";
print "[".¤tTime()."] starts running ...... \n";#->289
print "=========================================================================\n\n";
print $tmplog_fh "\n=========================================================================\n";
print $tmplog_fh "[".¤tTime()."] starts running ...... \n";#->289
print $tmplog_fh "=========================================================================\n\n";
} elsif ($StartOrFinishMessage eq "finishMessage") {
print "\n=========================================================================\n";
print "[".¤tTime()."] finished running .......\n";#->289
print "=========================================================================\n\n";
print $tmplog_fh "\n=========================================================================\n";
print $tmplog_fh "[".¤tTime()."] finished running .......\n";#->289
print $tmplog_fh "=========================================================================\n\n";
}
}
sub readParameters {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 0_startingTasks|105
# secondaryAppearInSection: >none
# input: none
# output: $long_ctss_bed_path, $outDir, $outputPrefix, $overwrite, $subsample_num
# toCall: my ($long_ctss_bed_path, $subsample_num, $outputPrefix, $outDir, $overwrite) = &readParameters();
# calledInLine: 108
#....................................................................................................................................................#
my ($long_ctss_bed_path, $subsample_num, $outputPrefix, $outDir, $overwrite);
$overwrite = 'no';
GetOptions (
"long_ctss_bed_path=s" => \$long_ctss_bed_path,
"subsample_num=s" => \$subsample_num,
"outputPrefix=s" => \$outputPrefix,
"outDir:s" => \$outDir,
"overwrite:s" => \$overwrite,
'help' => sub { HelpMessage(0) },
) or HelpMessage(1);
HelpMessage(1) unless $long_ctss_bed_path;
#---check file
my $file_check_hsh_ref = {
'long_ctss_bed_path' => $long_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;
}
chop $outDir if ($outDir =~ m/\/$/); #---remove the last slash
system "mkdir -p -m 755 $outDir/";
return($long_ctss_bed_path, $subsample_num, $outputPrefix, $outDir, $overwrite);
}
sub reportAndLogStatus {
#....................................................................................................................................................#
# subroutineCategory: log
# dependOnSub: currentTime|289
# appearInSub: checkAllExecutable|189, getTargetFraction|307, subsampleCTSS|590
# primaryAppearInSection: >none
# secondaryAppearInSection: 3_subsample|138
# input: $lineEnd, $message, $numTrailingSpace
# output:
# toCall: &reportAndLogStatus($message, $numTrailingSpace, $lineEnd);
# calledInLine: 212, 217, 226, 235, 244, 253, 262, 271, 280, 320, 338, 339, 342, 343, 344, 345, 653
#....................................................................................................................................................#
my ($message, $numTrailingSpace, $lineEnd) = @_;
my $trailingSpaces = '';
$trailingSpaces .= " " for (1..$numTrailingSpace);
print "[".¤tTime()."] ".$message.$trailingSpaces.$lineEnd;#->289
print $tmplog_fh "[".¤tTime()."] ".$message.$lineEnd if $lineEnd ne "\r";#->289
return ();
}
sub subsampleCTSS {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|568
# appearInSub: >none
# primaryAppearInSection: 3_subsample|138
# secondaryAppearInSection: >none
# input: $bedtools_bin, $long_ctss_bed_path, $outputPrefix, $result_bed_dir, $target_fraction
# output:
# toCall: &subsampleCTSS($long_ctss_bed_path, $result_bed_dir, $bedtools_bin, $target_fraction, $outputPrefix);
# calledInLine: 143
#....................................................................................................................................................#
my ($long_ctss_bed_path, $result_bed_dir, $bedtools_bin, $target_fraction, $tabix_bin, $bgzip_bin, $max_thread, $outputPrefix) = @_;
my $sub_collapse_ctss_bed_path = "$result_bed_dir/$outputPrefix.subsample.collapse.ctss.bed";
my $sub_ung_collapse_ctss_bed_path = "$result_bed_dir/$outputPrefix.subsample.unencoded_G.collapse.ctss.bed";
my $sub_long_ctss_bed_path = "$result_bed_dir/$outputPrefix.subsample.long.ctss.bed";
my $num_proc = 0;
my $tmp_CTSS_hsh_ref = {};
my $last_chrom = 'initial';
my $last_start = 'initial';
my $last_strand = 'initial';
if ($long_ctss_bed_path =~ m/\.gz$/) {
open (INCTSS, " gzip -dc $long_ctss_bed_path|");
} else {
open (INCTSS, "<", $long_ctss_bed_path);
}
open OUTCOLLAPSECTSS, ">", $sub_collapse_ctss_bed_path;
open OUTUNGCOLLAPSECTSS, ">", $sub_ung_collapse_ctss_bed_path;
open OUTLONGCTSS, ">", $sub_long_ctss_bed_path;
while (<INCTSS>) {
chomp;
my ($chrom, $start, $end, $MAPQ, $num_unencoded_G, $strand) = split /\t/;
next if (rand() > $target_fraction);
print OUTLONGCTSS join "", (join "\t", ($chrom, $start, $end, $MAPQ, $num_unencoded_G, $strand)), "\n";
$tmp_CTSS_hsh_ref->{$chrom}{$start}{$strand}{'all'}++;
$tmp_CTSS_hsh_ref->{$chrom}{$start}{$strand}{'ung'}++ if $num_unencoded_G > 0;
if ($last_chrom eq 'initial') {
$last_chrom = $chrom;
$last_start = $start;
$last_strand = $strand;
}
if (($chrom ne $last_chrom or $start ne $last_start or $strand ne $last_strand)) {
my $last_end = $last_start + 1;
my $num_total_ctss = $tmp_CTSS_hsh_ref->{$last_chrom}{$last_start}{$last_strand}{'all'};
print OUTCOLLAPSECTSS join "", (join "\t", ($last_chrom, $last_start, $last_end, $num_total_ctss, $num_total_ctss, $last_strand)), "\n";
if (exists $tmp_CTSS_hsh_ref->{$last_chrom}{$last_start}{$last_strand}{'ung'}) {
my $num_ung_ctss = $tmp_CTSS_hsh_ref->{$last_chrom}{$last_start}{$last_strand}{'ung'};
print OUTUNGCOLLAPSECTSS join "", (join "\t", ($last_chrom, $last_start, $last_end, $num_total_ctss, $num_ung_ctss, $last_strand)), "\n";
}
delete $tmp_CTSS_hsh_ref->{$last_chrom}{$last_start}{$last_strand};
$last_chrom = $chrom;
$last_start = $start;
$last_strand = $strand;
$num_proc++;
if ($num_proc%10000 == 0) {
&reportAndLogStatus("$num_proc CTSS piled up", 10, "\n");#->568
}
}
if (eof(INCTSS)) {
foreach my $chrom (sort keys %{$tmp_CTSS_hsh_ref}) {
foreach my $start (sort {$a <=> $b} keys %{$tmp_CTSS_hsh_ref->{$chrom}}) {
my $end = $start + 1;
foreach my $strand (sort keys %{$tmp_CTSS_hsh_ref->{$chrom}{$start}}) {
my $num_total_ctss = $tmp_CTSS_hsh_ref->{$chrom}{$start}{$strand}{'all'};
print OUTCOLLAPSECTSS join "", (join "\t", ($chrom, $start, $end, $num_total_ctss, $num_total_ctss, $strand)), "\n";
if (exists $tmp_CTSS_hsh_ref->{$chrom}{$start}{$strand}{'ung'}) {
my $num_ung_ctss = $tmp_CTSS_hsh_ref->{$chrom}{$start}{$strand}{'ung'};
print OUTUNGCOLLAPSECTSS join "", (join "\t", ($chrom, $start, $end, $num_total_ctss, $num_ung_ctss, $strand)), "\n";
}
}
}
}
}
}
close INCTSS;
close OUTCOLLAPSECTSS;
close OUTUNGCOLLAPSECTSS;
my $ctss_hsh_ref = {
'sub_collapse_ctss_bed_path' => $sub_collapse_ctss_bed_path,
'sub_ung_collapse_ctss_bed_path' => $sub_ung_collapse_ctss_bed_path,
'sub_long_ctss_bed_path' => $sub_long_ctss_bed_path,
};
foreach my $ctss_name (sort keys %{$ctss_hsh_ref}) {
my $ctss_path = $ctss_hsh_ref->{$ctss_name};
my $tabix_ctss_path = "$ctss_path.gz";
&reportAndLogStatus("Compressing $ctss_name.", 10, "\n");#->1991
system "$bgzip_bin -@ $max_thread -c $ctss_path >$tabix_ctss_path";
system "rm -f $ctss_path";
&reportAndLogStatus("Tabix indexing $ctss_name.", 10, "\n");#->1991
system "$tabix_bin -p bed $tabix_ctss_path";
}
return ();
}
sub timeStamp {
#....................................................................................................................................................#
# subroutineCategory: time, general
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: >none
# secondaryAppearInSection: >none
# input: none
# output: $curntTimeStamp
# toCall: my ($curntTimeStamp) = &timeStamp();
# calledInLine: 93
#....................................................................................................................................................#
my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst)=localtime(time);
my $curntTimeStamp = sprintf "%04d.%02d.%02d.%02d.%02d.%02d", $year+1900,$mon+1,$mday,$hour,$min,$sec;
return ($curntTimeStamp);
}
exit;