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scafe.workflow.bk.solo
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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 Getopt::Long 'HelpMessage';
use Time::HiRes qw( time );
use File::Spec::Functions qw(rel2abs abs2rel);
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.workflow.bk.solo <---
<--- workflow, bulk mode, process a single sample --->
Description:
This workflow process a single sample, from a bulk CAGE bam file to read count per tCRE
Usage:
scafe.workflow.bk.solo [options] --run_bam_path --genome --run_tag --run_outDir
--run_bam_path <required> [string] bam file (of CAGE reads), can be read 1 only or pair-end
--genome <required> [string] name of genome reference, e.g. hg19.gencode_v32lift37
--run_tag <required> [string] prefix for the output files
--run_outDir <required> [string] directory for the output files
--training_signal_path (optional) [string] quantitative signal (e.g. ATAC -logP, in bigwig format), or binary genomic
regions (e.g. annotated CRE, in bed format) used for training of logical
regression model If null, $usr_glm_model_path must be supplied for
pre-built logical regression model. It overrides usr_glm_model_path
(default=null)
--testing_signal_path (optional) [string] quantitative signal (e.g. ATAC -logP, in bigwig format), or binary genomic
regions (e.g. annotated CRE, in bed format) used for testing the performance
of the logical regression model. If null, annotated TSS from $genome will be
used as binary genomic regions. (default=null)
--max_thread (optional) [integer] maximum number of parallel threads, capped at 10 to
avoid memory overflow (default=5)
--overwrite (optional) [yes/no] erase run_outDir before running (default=no)
Dependencies:
R packages: 'ROCR','PRROC', 'caret', 'e1071', 'ggplot2', 'scales', 'reshape2'
bigWigAverageOverBed
bedGraphToBigWig
bedtools
samtools
paraclu
paraclu-cut.sh
tabix
bgzip
For demo, cd to SCAFE dir and run,
scafe.workflow.bk.solo \
--overwrite=yes \
--run_bam_path=./demo/input/bk.solo/demo.CAGE.bam \
--genome=hg19.gencode_v32lift37 \
--run_tag=demo \
--run_outDir=./demo/output/bk.solo/
=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>
#<\global>
#====================================================================================================================================================#
#====================================================================================================================================================#
{ #Main sections lexical scope starts
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 0_startTasks
#
#<section ID="startTasks" num="0">
my $ARGV_ary_ref = [@ARGV];
my ($run_bam_path, $genome, $training_signal_path, $testing_signal_path, $max_thread, $run_tag, $run_outDir, $overwrite) = &readParameters();#->374
$max_thread = 10 if $max_thread > 10;
my ($scafe_dir, $script_dir, $result_script_dir, $ARGVStr, $scriptAbsPath) = &prepDir($run_outDir, $ARGV_ary_ref);#->346
&logCalledCMDAndScript($ARGVStr, $result_script_dir, $scriptAbsPath);#->321
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
# section 1_run
#
#<section ID="run" num="1">
my ($path_hsh_ref) = &define_path($run_outDir, $run_tag, $run_bam_path, $training_signal_path, $testing_signal_path, $script_dir);#->165
my ($task_info_hsh_ref) = &define_task($genome, $path_hsh_ref, $max_thread, $run_tag, $run_outDir);#->206
&run_task($task_info_hsh_ref, $path_hsh_ref, $result_script_dir);#->424
#<\section>
#====================================================================================================================================================#
#====================================================================================================================================================#
} #Main sections lexical scope ends
#====================================================================================================================================================#
#====================================================================================================================================================#
#List of subroutines by category
#
# general [n=3]:
# currentTime, logCalledCMDAndScript, readParameters
#
# unassigned [n=4]:
# define_path, define_task, prepDir
# run_task
#
#====================================================================================================================================================#
sub currentTime {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: >none
# appearInSub: prepDir|346
# primaryAppearInSection: >none
# secondaryAppearInSection: 0_startTasks|109
# input: none
# output: $runTime
# toCall: my ($runTime) = ¤tTime();
# calledInLine: 360
#....................................................................................................................................................#
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 define_path {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 1_run|121
# secondaryAppearInSection: >none
# input: $run_bam_path, $run_outDir, $run_tag, $script_dir, $testing_signal_path, $training_signal_path
# output: $path_hsh_ref
# toCall: my ($path_hsh_ref) = &define_path($run_outDir, $run_tag, $run_bam_path, $training_signal_path, $testing_signal_path, $script_dir);
# calledInLine: 124
#....................................................................................................................................................#
my ($run_outDir, $run_tag, $run_bam_path, $training_signal_path, $testing_signal_path, $script_dir) = @_;
my $path_hsh_ref = {
'script_dir' => $script_dir,
'run_bam_path' => $run_bam_path,
'training_signal_path' => $training_signal_path,
'testing_signal_path' => $testing_signal_path,
'long_ctss_bed_path' => $run_outDir."/bam_to_ctss/".$run_tag."/bed/".$run_tag.".long.ctss.bed.gz",
'ung_ctss_bed_path' => $run_outDir."/bam_to_ctss/".$run_tag."/bed/".$run_tag.".unencoded_G.collapse.ctss.bed.gz",
'collapse_ctss_bed_path' => $run_outDir."/bam_to_ctss/".$run_tag."/bed/".$run_tag.".collapse.ctss.bed.gz",
'raw_tssCluster_bed_path' => $run_outDir."/cluster/".$run_tag."/bed/".$run_tag.".tssCluster.bed.gz",
'filtered_tssCluster_info_path' => $run_outDir."/filter/".$run_tag."/log/".$run_tag.".tssCluster.log.tsv",
'bw_cpm_rev_path' => $run_outDir."/ctss_to_bigwig/".$run_tag."/wig/".$run_tag.".cpm.rev.bw",
'bw_cpm_fwd_path' => $run_outDir."/ctss_to_bigwig/".$run_tag."/wig/".$run_tag.".cpm.fwd.bw",
'bw_count_rev_path' => $run_outDir."/ctss_to_bigwig/".$run_tag."/wig/".$run_tag.".count.rev.bw",
'bw_count_fwd_path' => $run_outDir."/ctss_to_bigwig/".$run_tag."/wig/".$run_tag.".count.fwd.bw",
'tCRE_bed_path' => $run_outDir."/annotate/".$run_tag."/bed/".$run_tag.".CRE.coord.bed.gz",
'tCRE_info_path' => $run_outDir."/annotate/".$run_tag."/log/".$run_tag.".CRE.info.tsv.gz",
'tssCluster_bed_path' => $run_outDir."/annotate/".$run_tag."/bed/".$run_tag.".cluster.coord.bed.gz",
'tssCluster_info_path' => $run_outDir."/annotate/".$run_tag."/log/".$run_tag.".cluster.info.tsv.gz",
'directionality_info_path' => $run_outDir."/directionality/".$run_tag."/log/".$run_tag.".directionality.log.tsv.gz",
};
foreach my $level (qw/robust lenient default/) {
$path_hsh_ref->{"$level.filtered_tssCluster_bed_path"} = $run_outDir."/filter/".$run_tag."/bed/".$run_tag.".tssCluster.".$level.".filtered.bed.gz";
}
return ($path_hsh_ref);
}
sub define_task {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 1_run|121
# secondaryAppearInSection: >none
# input: $genome, $max_thread, $path_hsh_ref, $run_outDir, $run_tag
# output: $task_info_hsh_ref
# toCall: my ($task_info_hsh_ref) = &define_task($genome, $path_hsh_ref, $max_thread, $run_tag, $run_outDir);
# calledInLine: 125
#....................................................................................................................................................#
my ($genome, $path_hsh_ref, $max_thread, $run_tag, $run_outDir) = @_;
my $task_info_hsh_ref = {
1 => {
'task_name' => 'bam_to_ctss',
'script_name' => 'scafe.tool.bk.bam_to_ctss',
'param' => [
['genome', $genome],
['max_thread', $max_thread],
['bamPath', $path_hsh_ref->{'run_bam_path'}],
['outputPrefix', $run_tag],
['outDir', $run_outDir."/bam_to_ctss"],
],
'check' => [
$path_hsh_ref->{'ung_ctss_bed_path'},
$path_hsh_ref->{'collapse_ctss_bed_path'},
$path_hsh_ref->{'long_ctss_bed_path'},
]
},
2 => {
'task_name' => 'cluster',
'script_name' => 'scafe.tool.cm.cluster',
'param' => [
['cluster_ctss_bed_path', $path_hsh_ref->{'collapse_ctss_bed_path'}],
['count_ctss_bed_path_list', $path_hsh_ref->{'collapse_ctss_bed_path'}],
['count_scope_bed_path', $path_hsh_ref->{'collapse_ctss_bed_path'}],
['outputPrefix', $run_tag],
['outDir', $run_outDir."/cluster"],
],
'check' => [
$path_hsh_ref->{'raw_tssCluster_bed_path'},
]
},
3 => {
'task_name' => 'filter',
'script_name' => 'scafe.tool.cm.filter',
'param' => [
['genome', $genome],
['training_signal_path', $path_hsh_ref->{'training_signal_path'}],
['testing_signal_path', $path_hsh_ref->{'testing_signal_path'}],
['ung_ctss_bed_path', $path_hsh_ref->{'ung_ctss_bed_path'}],
['tssCluster_bed_path', $path_hsh_ref->{'raw_tssCluster_bed_path'}],
['ctss_bed_path', $path_hsh_ref->{'collapse_ctss_bed_path'}],
['outputPrefix', $run_tag],
['outDir', $run_outDir."/filter"],
],
'check' => [
$path_hsh_ref->{'default.filtered_tssCluster_bed_path'},
$path_hsh_ref->{'robust.filtered_tssCluster_bed_path'},
$path_hsh_ref->{'lenient.filtered_tssCluster_bed_path'},
]
},
4 => {
'task_name' => 'ctss_to_bigwig',
'script_name' => 'scafe.tool.cm.ctss_to_bigwig',
'param' => [
['genome', $genome],
['ctss_bed_path', $path_hsh_ref->{'collapse_ctss_bed_path'}],
['outputPrefix', $run_tag],
['outDir', $run_outDir."/ctss_to_bigwig"],
],
'check' => [
$path_hsh_ref->{'bw_cpm_rev_path'},
$path_hsh_ref->{'bw_cpm_fwd_path'},
$path_hsh_ref->{'bw_count_rev_path'},
$path_hsh_ref->{'bw_count_fwd_path'},
]
},
5 => {
'task_name' => 'annotate',
'script_name' => 'scafe.tool.cm.annotate',
'param' => [
['genome', $genome],
['tssCluster_bed_path', $path_hsh_ref->{"default.filtered_tssCluster_bed_path"}],
['tssCluster_info_path', $path_hsh_ref->{'filtered_tssCluster_info_path'}],
['outputPrefix', $run_tag],
['outDir', $run_outDir."/annotate"],
],
'check' => [
$path_hsh_ref->{"tCRE_bed_path"},
$path_hsh_ref->{"tCRE_info_path"},
$path_hsh_ref->{"tssCluster_bed_path"},
$path_hsh_ref->{"tssCluster_info_path"},
]
},
6 => {
'task_name' => 'count',
'script_name' => 'scafe.tool.bk.count',
'param' => [
['countRegion_bed_path', $path_hsh_ref->{"tCRE_bed_path"}],
['ctss_bed_path', $path_hsh_ref->{'collapse_ctss_bed_path'}],
['outputPrefix', $run_tag],
['outDir', $run_outDir."/count"],
],
'check' => [
$run_outDir."/count/$run_tag/log/count.log.tsv",
]
},
7 => {
'task_name' => 'directionality',
'script_name' => 'scafe.tool.cm.directionality',
'param' => [
['CRE_bed_path', $path_hsh_ref->{'tCRE_bed_path'}],
['CRE_info_path', $path_hsh_ref->{'tCRE_info_path'}],
['ctss_bed_path', $path_hsh_ref->{'collapse_ctss_bed_path'}],
['outputPrefix', $run_tag],
['outDir', $run_outDir."/directionality"],
],
'check' => [
$path_hsh_ref->{"directionality_info_path"},
]
}
};
return($task_info_hsh_ref);
}
sub logCalledCMDAndScript {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 0_startTasks|109
# secondaryAppearInSection: >none
# input: $ARGVStr, $result_script_dir, $scriptAbsPath
# output:
# toCall: &logCalledCMDAndScript($ARGVStr, $result_script_dir, $scriptAbsPath);
# calledInLine: 116
#....................................................................................................................................................#
my ($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 prepDir {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: currentTime|147
# appearInSub: >none
# primaryAppearInSection: 0_startTasks|109
# secondaryAppearInSection: >none
# input: $ARGV_ary_ref, $run_outDir
# output: $ARGVStr, $result_script_dir, $scafe_dir, $scriptAbsPath, $script_dir
# toCall: my ($scafe_dir, $script_dir, $result_script_dir, $ARGVStr, $scriptAbsPath) = &prepDir($run_outDir, $ARGV_ary_ref);
# calledInLine: 115
#....................................................................................................................................................#
my ($run_outDir, $ARGV_ary_ref) = @_;
my $scriptAbsPath = abs_path($0);
my $ARGVStr = join "\n", (¤tTime(), $scriptAbsPath, @{$ARGV_ary_ref});#->147
my @path_split = split /\//, $scriptAbsPath;
my $scafe_dir_index = $#path_split-2;
my $script_dir_index = $#path_split-1;
my $scafe_dir = join "/", @path_split[0..$scafe_dir_index];
my $script_dir = join "/", @path_split[0..$script_dir_index];
my @mkDirAry;
my $result_script_dir = "$run_outDir/script/"; push @mkDirAry, $result_script_dir;
foreach my $dir (@mkDirAry) {system ("mkdir -pm 755 $dir");}
return ($scafe_dir, $script_dir, $result_script_dir, $ARGVStr, $scriptAbsPath);
}
sub readParameters {
#....................................................................................................................................................#
# subroutineCategory: general
# dependOnSub: >none
# appearInSub: >none
# primaryAppearInSection: 0_startTasks|109
# secondaryAppearInSection: >none
# input: none
# output: $genome, $max_thread, $overwrite, $run_bam_path, $run_outDir, $run_tag, $testing_signal_path, $training_signal_path
# toCall: my ($run_bam_path, $genome, $training_signal_path, $testing_signal_path, $max_thread, $run_tag, $run_outDir, $overwrite) = &readParameters();
# calledInLine: 113
#....................................................................................................................................................#
my ($run_bam_path, $genome, $training_signal_path, $testing_signal_path, $max_thread, $run_tag, $run_outDir, $overwrite);
$overwrite = 'no';
$max_thread = 5;
GetOptions (
"run_bam_path=s" => \$run_bam_path,
"genome=s" => \$genome,
"max_thread:i" => \$max_thread,
"training_signal_path:s" => \$training_signal_path,
"testing_signal_path:s" => \$testing_signal_path,
"run_tag=s" => \$run_tag,
"run_outDir=s" => \$run_outDir,
"overwrite:s" => \$overwrite,
'help' => sub { HelpMessage(0) },
) or HelpMessage(1);
HelpMessage(1) unless $run_bam_path;
#---check file
my $file_check_hsh_ref = {
'run_bam_path' => $run_bam_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;
}
system "rm -rf $run_outDir" if ($overwrite eq 'yes');
chop $run_outDir if ($run_outDir =~ m/\/$/); #---remove the last slash
system "mkdir -p -m 755 $run_outDir/";
return($run_bam_path, $genome, $training_signal_path, $testing_signal_path, $max_thread, $run_tag, $run_outDir, $overwrite);
}
sub run_task {
#....................................................................................................................................................#
# subroutineCategory: unassigned
# dependOnSub: currentTime|141
# appearInSub: >none
# primaryAppearInSection: 1_run|115
# secondaryAppearInSection: >none
# input: $path_hsh_ref, $result_script_dir, $task_info_hsh_ref
# output: none
# toCall: &run_task($task_info_hsh_ref, $path_hsh_ref, $result_script_dir);
# calledInLine: 120
#....................................................................................................................................................#
my ($task_info_hsh_ref, $path_hsh_ref, $result_script_dir) = @_;
open TASKLOG, ">", "$result_script_dir/task.log.txt";
print TASKLOG join "", (join "\t", ('0', 'workflow', 'manager', 'started', ¤tTime())), "\n";#->141
foreach my $task_num (sort {$a <=> $b} keys %{$task_info_hsh_ref}) {
my $task_name = $task_info_hsh_ref->{$task_num}{'task_name'};
my $script_name = $task_info_hsh_ref->{$task_num}{'script_name'};
my $result_found = 'yes';
foreach my $check_path (@{$task_info_hsh_ref->{$task_num}{'check'}}) {
$result_found = 'no' if not -s $check_path;
}
if ($result_found eq 'no') {
print "\n";
print "#===========================#\n";
print "Start running $task_name\n";
print "#===========================#\n";
print TASKLOG join "", (join "\t", ($task_num, $task_name, $script_name, 'started', ¤tTime())), "\n";#->141
my $script_path = $path_hsh_ref->{'script_dir'}.'/'.$script_name;
die "script of $task_name does not exist at $script_path\n" if not -s $script_path;
my @cmd_param_ary = ($script_path);
foreach my $indiv_param_ary_ref (@{$task_info_hsh_ref->{$task_num}{'param'}}) {
my ($param_name, $param_val) = @{$indiv_param_ary_ref};
if (defined $param_val) {#---[2020/10/07 20:32] specifically for skipping training_signal_path if not input
push @cmd_param_ary, "--$param_name=$param_val";
}
}
my $cmd = join " ", @cmd_param_ary;
system "$cmd";
$result_found = 'yes';
foreach my $check_path (@{$task_info_hsh_ref->{$task_num}{'check'}}) {
$result_found = 'no' if not -s $check_path;
}
if ($result_found eq 'yes') {
print "\n";
print "#============================================#\n";
print "Results of $task_name found. Run successfully.\n";
print "#============================================#\n";
print TASKLOG join "", (join "\t", ($task_num, $task_name, $script_name, 'successful', ¤tTime())), "\n";#->141
} else {
print TASKLOG join "", (join "\t", ($task_num, $task_name, $script_name, 'failed', ¤tTime())), "\n";#->141
print TASKLOG join "", (join "\t", ('0', 'workflow', 'workflow', 'failed', ¤tTime())), "\n";#->141
print "\n";
print "#========================================#\n";
print "Results of $task_name not found. Quitting.\n";
print "#========================================#\n";
die;
}
} else {
print "#=====================================#\n";
print "Results of $task_name found. Skipping.\n";
print "#=====================================#\n";
}
}
print "\n";
print "#=====================================================#\n";
print "Results of all tasks found. All tasks run successfully.\n";
print "#=====================================================#\n";
print TASKLOG join "", (join "\t", ('0', 'workflow', 'manager', 'successful', ¤tTime())), "\n";#->141
close TASKLOG;
}
exit;