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scafe.tool.cm.ctss_to_bigwig
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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;
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.ctss_to_bigwig <---
<--- tool, common mode, convert ctss to bigwig --->
Description:
This tool converts a ctss bed file into two bigwig file, one for each strand, for visualization purpose
Usage:
scafe.tool.cm.ctss_to_bigwig [options] --ctss_bed_path --genome --outputPrefix --outDir
--ctss_bed_path <required> [string] "collapse" ctss file from scafe.tool.sc.bam_to_ctss.pl
--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
--overwrite (optional) [yes/no] erase outDir/outputPrefix before running (default=no)
Dependencies:
bedGraphToBigWig
For demo, cd to SCAFE dir and run,
scafe.tool.cm.ctss_to_bigwig \
--ctss_bed_path=./demo/output/sc.solo/bam_to_ctss/demo/bed/demo.collapse.ctss.bed.gz \
--genome=hg19.gencode_v32lift37 \
--outputPrefix=demo \
--outDir=./demo/output/sc.solo/ctss_to_bigwig/
=head1 VERSION
v0.9.0-beta [March 20, 2021]
-Initial pre-release
v1.0.0 [June 6, 2022]
-No update
=cut#
#<\doc>
#====================================================================================================================================================#
#====================================================================================================================================================#
#<lastCmdCalled>
#
# notCalledBefore
#
# notCalledBefore
#
#<\lastCmdCalled>
#====================================================================================================================================================#
#====================================================================================================================================================#
#<global>
my $scriptDirPath = dirname(rel2abs($0));
my $scriptAbsPath = abs_path($0);
my ($curntTimeStamp) = &timeStamp();#->675
my $ARGVStr = join "\n", (¤tTime(), $scriptAbsPath, @ARGV);#->385
my $globalReadmeHsh_ref = {};
our $tmplog_fh;
#<\global>
#====================================================================================================================================================#
#====================================================================================================================================================#
{ #Main sections lexical scope starts
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 0_startingTasks
#
#<section ID="startingTasks" num="0">
my ($ctss_bed_path, $genome, $outputPrefix, $outDir) = &readParameters();#->613
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 1_defineHardCodedParam
#
#<section ID="defineHardCodedParam" num="1">
my $paramTag = "$outputPrefix";
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 2_defineOutDirPath
#
#<section ID="defineOutDirPath" num="2">
my @mkDirAry;
my $result_dir = "$outDir/$paramTag/"; push @mkDirAry, $result_dir;
my $result_bed_dir = "$result_dir/bed/"; push @mkDirAry, $result_bed_dir;
my $result_wig_dir = "$result_dir/wig/"; push @mkDirAry, $result_wig_dir;
my $result_script_dir = "$result_dir/script/"; push @mkDirAry, $result_script_dir;
#my $resultEdgeRDir = "$result_dir/edgeR/"; push @mkDirAry, $resultEdgeRDir;
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, $scriptAbsPath);#->434
&printStartOrFinishMessage("startMessage");#->579
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 3_count
#
#<section ID="count" num="3">
my ($tabix_bin, $bgzip_bin, $bedtools_bin, $samtools_bin, $paraclu_bin, $cut_sh_path, $bedGraphToBigWig_bin, $bigWigAverageOverBed_bin) = &checkAllExecutable();#->183
my ($chrom_size_path) = &checkChromSizePath($genome);#->283
my ($total_count) = &getTotalCount($ctss_bed_path);#->403
&convertCTSS($ctss_bed_path, $result_wig_dir, $result_bed_dir, $outputPrefix, $chrom_size_path, $bedGraphToBigWig_bin, $total_count);#->303
system ("rm -r $result_bed_dir");
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 4_finishingTasks
#
#<section ID="finishingTasks" num="4">
&printOutputFileListAndReadme($ARGVStr, $paramTag, $outDir);#->459
&printStartOrFinishMessage("finishMessage");#->579
#<\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
#
# range [n=1]:
# convertCTSS
#
# time [n=1]:
# timeStamp
#
# unassigned [n=3]:
# checkAllExecutable, checkChromSizePath, getTotalCount
#
#====================================================================================================================================================#
sub checkAllExecutable {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|653
# appearInSub: >none
# primaryAppearInSection: 3_count|134
# 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: 137
#....................................................................................................................................................#
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");#->653
{
my $stdOut = `$tabix_bin --version 2>&1`;
if ($stdOut =~ m/tabix \(htslib\) (\S+)/) {
&reportAndLogStatus("Checking: tabix version: $1", 0, "\n");#->653
} 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");#->653
} 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");#->653
} 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");#->653
} 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");#->653
} 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");#->653
} 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");#->653
} else {
die "bedGraphToBigWig not installed properly. Quitting.\n";
}
}
{
my $stdOut = `$bigWigAverageOverBed_bin 2>&1`;
if ($stdOut =~ m/bigWigAverageOverBed v(\S+)/) {
&reportAndLogStatus("Checking: bigWigAverageOverBed version: $1", 0, "\n");#->653
} else {
die "bigWigAverageOverBed is not installed properly. Quitting.\n";
}
}
return ($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_count|134
# secondaryAppearInSection: >none
# input: $genome
# output: $chrom_size_path
# toCall: my ($chrom_size_path) = &checkChromSizePath($genome);
# calledInLine: 138
#....................................................................................................................................................#
my ($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 convertCTSS {
#....................................................................................................................................................#
# subroutineCategory: range
# dependOnSub: reportAndLogStatus|653
# appearInSub: >none
# primaryAppearInSection: 3_count|134
# secondaryAppearInSection: >none
# input: $bedGraphToBigWig_bin, $chrom_size_path, $ctss_bed_path, $outputPrefix, $result_bed_dir, $result_wig_dir, $total_count
# output:
# toCall: &convertCTSS($ctss_bed_path, $result_wig_dir, $result_bed_dir, $outputPrefix, $chrom_size_path, $bedGraphToBigWig_bin, $total_count);
# calledInLine: 140
#....................................................................................................................................................#
my ($ctss_bed_path, $result_wig_dir, $result_bed_dir, $outputPrefix, $chrom_size_path, $bedGraphToBigWig_bin, $total_count) = @_;
my %strand_mode_hsh = (
'fwd.count' => ['fwd', '+', 'count'],
'rev.count' => ['rev', '-', 'count'],
'fwd.cpm' => ['fwd', '+', 'cpm'],
'rev.cpm' => ['rev', '-', 'cpm'],
);
my %threadHsh =();
foreach my $strand_mode (keys %strand_mode_hsh) {
my ($fwd_rev, $strand, $mode) = @{$strand_mode_hsh{$strand_mode}};
($threadHsh{$strand_mode}) = threads->new(#---refer to http://www.perlmonks.org/?node_id=966781, the
sub {
my ($fwd_rev, $strand, $mode) = @_;
my $bedGraphPath = "$result_bed_dir/$outputPrefix.$mode.$fwd_rev.bedGraph";
my $bigwigPath = "$result_wig_dir/$outputPrefix.$mode.$fwd_rev.bw";
my @pipeToBedGraphAry = ();
if ($ctss_bed_path =~ m/\.gz$/) {
push @pipeToBedGraphAry, "gzip -dc $ctss_bed_path | sort -k1,1 -k2,2n |";
} else {
push @pipeToBedGraphAry, "cat $ctss_bed_path | sort -k1,1 -k2,2n |";
}
push @pipeToBedGraphAry, "grep \"$strand\" |";
push @pipeToBedGraphAry, "cut -f 1,2,3,5 |";
&reportAndLogStatus("printing bedgraph for $strand strand in $mode mode", 10, "\n");#->653
my $pipeToBedGraphCmd = join " ", @pipeToBedGraphAry;
open (OUTBEDGRAPH, ">", $bedGraphPath);
open (INBEDGRAPH, $pipeToBedGraphCmd);
while (<INBEDGRAPH>) {
chomp;
my ($chrom, $chromStart, $chromEnd, $count) = split /\t/;
my $score = $count;
$score = sprintf "%.2e", $count/($total_count/1000000) if $mode eq 'cpm';
print OUTBEDGRAPH join "", (join "\t", ($chrom, $chromStart, $chromEnd, $score)), "\n";
}
close INBEDGRAPH;
close OUTBEDGRAPH;
&reportAndLogStatus("converting bedgraph to bigwig $strand strand $mode mode", 10, "\n");#->653
system ("$bedGraphToBigWig_bin $bedGraphPath $chrom_size_path $bigwigPath;");
&reportAndLogStatus("removing bedgraph", 10, "\n");#->653
system ("rm -f $bedGraphPath;");
return ();
}
,($fwd_rev, $strand, $mode)
);
}
while (keys %threadHsh) {
foreach my $strand (keys %threadHsh) {
my $thr = $threadHsh{$strand};
if (not $thr->is_running()) {
$thr->join;
delete $threadHsh{$strand};
}
}
sleep 1;
}
return ();
}
sub currentTime {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: >none
# appearInSub: printStartOrFinishMessage|579, reportAndLogStatus|653
# primaryAppearInSection: >none
# secondaryAppearInSection: 2_defineOutDirPath|115, 4_finishingTasks|146
# input: none
# output: $runTime
# toCall: my ($runTime) = ¤tTime();
# calledInLine: 88, 595, 599, 604, 608, 669, 670
#....................................................................................................................................................#
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 getTotalCount {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: reportAndLogStatus|653
# appearInSub: >none
# primaryAppearInSection: 3_count|134
# secondaryAppearInSection: >none
# input: $ctss_bed_path
# output: $total_count
# toCall: my ($total_count) = &getTotalCount($ctss_bed_path);
# calledInLine: 139
#....................................................................................................................................................#
my ($ctss_bed_path) = @_;
&reportAndLogStatus("getting total count", 10, "\n");#->653
my $total_count = 0;
if ($ctss_bed_path =~ m/\.gz$/) {
open CTSS, "gzip -dc $ctss_bed_path | cut -f 5 |";
} else {
open CTSS, "cut -f 5 $ctss_bed_path |";
}
while (<CTSS>) {
chomp;
$total_count+=$_;
}
close CTSS;
&reportAndLogStatus("total count = $total_count", 10, "\n");#->653
return ($total_count);
}
sub logCalledCMDAndScript {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 2_defineOutDirPath|115
# secondaryAppearInSection: >none
# input: $ARGVStr, $result_script_dir, $scriptAbsPath
# output:
# toCall: &logCalledCMDAndScript($ARGVStr, $result_script_dir, $scriptAbsPath);
# calledInLine: 128
#....................................................................................................................................................#
my ($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: 4_finishingTasks|146
# secondaryAppearInSection: >none
# input: $ARGVStr, $outDir, $paramTag
# output:
# toCall: &printOutputFileListAndReadme($ARGVStr, $paramTag, $outDir);
# calledInLine: 149
#....................................................................................................................................................#
my ($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 $outputFilePath (sort keys %{$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->{$outputFilePath}{'headerAry'}});
@colLenCountHsh = sort {$b <=> $a} @colLenCountHsh;
my $headerColLen = $colLenCountHsh[0]+2;
print README "\n";
print README "\n";
print README "===================\n";
print README "Column descriptions\n";
print README "===================\n";
print README "\n";
printf README "%-".$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;
}
@{$filelistLenCountHsh{'dir'}} = sort {$b <=> $a} @{$filelistLenCountHsh{'dir'}};
@{$filelistLenCountHsh{'name'}} = sort {$b <=> $a} @{$filelistLenCountHsh{'name'}};
@{$filelistLenCountHsh{'description'}} = sort {$b <=> $a} @{$filelistLenCountHsh{'description'}};
my $fileDir_colLen = $filelistLenCountHsh{'dir'}[0]+2;
my $fileName_colLen = $filelistLenCountHsh{'name'}[0]+2;
my $fileDescription_colLen = $filelistLenCountHsh{'description'}[0]+2;
printf OUTFILELIST ("%-".$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|385
# appearInSub: >none
# primaryAppearInSection: 2_defineOutDirPath|115, 4_finishingTasks|146
# secondaryAppearInSection: >none
# input: $StartOrFinishMessage
# output: none
# toCall: &printStartOrFinishMessage($StartOrFinishMessage);
# calledInLine: 129, 150
#....................................................................................................................................................#
my ($StartOrFinishMessage) = @_;
if ($StartOrFinishMessage eq "startMessage") {
print "\n=========================================================================\n";
print "[".¤tTime()."] starts running ...... \n";#->385
print "=========================================================================\n\n";
print $tmplog_fh "\n=========================================================================\n";
print $tmplog_fh "[".¤tTime()."] starts running ...... \n";#->385
print $tmplog_fh "=========================================================================\n\n";
} elsif ($StartOrFinishMessage eq "finishMessage") {
print "\n=========================================================================\n";
print "[".¤tTime()."] finished running .......\n";#->385
print "=========================================================================\n\n";
print $tmplog_fh "\n=========================================================================\n";
print $tmplog_fh "[".¤tTime()."] finished running .......\n";#->385
print $tmplog_fh "=========================================================================\n\n";
}
}
sub readParameters {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 0_startingTasks|99
# secondaryAppearInSection: >none
# input: none
# output: $ctss_bed_path, $genome, $outDir, $outputPrefix
# toCall: my ($ctss_bed_path, $genome, $outputPrefix, $outDir) = &readParameters();
# calledInLine: 102
#....................................................................................................................................................#
my ($ctss_bed_path, $genome, $outputPrefix, $outDir);
GetOptions (
"ctss_bed_path=s" => \$ctss_bed_path,
"genome=s" => \$genome,
"outputPrefix=s" => \$outputPrefix,
"outDir:s" => \$outDir,
'help' => sub { HelpMessage(0) },
) or HelpMessage(1);
HelpMessage(1) unless $ctss_bed_path;
#---check file
my $file_check_hsh_ref = {
'ctss_bed_path' => $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 $outDir/";
return($ctss_bed_path, $genome, $outputPrefix, $outDir);
}
sub reportAndLogStatus {
#....................................................................................................................................................#
# subroutineCategory: log
# dependOnSub: currentTime|385
# appearInSub: checkAllExecutable|183, convertCTSS|303, getTotalCount|403
# primaryAppearInSection: >none
# secondaryAppearInSection: 3_count|134
# input: $lineEnd, $message, $numTrailingSpace
# output:
# toCall: &reportAndLogStatus($message, $numTrailingSpace, $lineEnd);
# calledInLine: 206, 211, 220, 229, 238, 247, 256, 265, 274, 345, 359, 362, 416, 429
#....................................................................................................................................................#
my ($message, $numTrailingSpace, $lineEnd) = @_;
my $trailingSpaces = '';
$trailingSpaces .= " " for (1..$numTrailingSpace);
print "[".¤tTime()."] ".$message.$trailingSpaces.$lineEnd;#->385
print $tmplog_fh "[".¤tTime()."] ".$message.$lineEnd if $lineEnd ne "\r";#->385
return ();
}
sub timeStamp {
#....................................................................................................................................................#
# subroutineCategory: time, general
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: >none
# secondaryAppearInSection: >none
# input: none
# output: $curntTimeStamp
# toCall: my ($curntTimeStamp) = &timeStamp();
# calledInLine: 87
#....................................................................................................................................................#
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;