scafe.download.resources.genome

#!/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;

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no strict 'refs';
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#====================================================================================================================================================#
#<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 
                           ---> download.resources.genome <---
                     <--- download, reference genome to resources dir --->

 Description:
   This script download reference genome data and save in ./resources/genome.

 Usage:
   download.resources.genome --genome
   
   --genome <required> [string] name of genome reference, currently available genomes:
                                hg19.gencode_v32lift37
                                hg38.gencode_v32
                                mm10.gencode_vM25
                                TAIR10.AtRTDv2

 Dependencies:
   wget
   tar

 For demo, cd to SCAFE dir and run,
   scafe.download.resources.genome \
   --genome=hg19.gencode_v32lift37

=head1 VERSION

v0.9.0-beta [March 20, 2021]
	-Initial pre-release

v1.0.0 [June 6, 2022]
	-No major update

=cut
#<\doc>
#====================================================================================================================================================#

#====================================================================================================================================================#
#<lastCmdCalled>
#
#	notCalledBefore
#
#	notCalledBefore
#
#<\lastCmdCalled>
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#====================================================================================================================================================#
#<global>
#<\global>
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#====================================================================================================================================================#
{	#Main sections lexical scope starts
#====================================================================================================================================================#

#====================================================================================================================================================#
#	section 0_startTasks
#
#<section ID="startTasks" num="0">
my $genome_url_hsh_ref = {
	'hg19.gencode_v32lift37' => "https://www.dropbox.com/s/ol23wpn695p06wj/hg19.gencode_v32lift37.tar.gz",
	'hg38.gencode_v32' => "https://www.dropbox.com/s/q9h4dcz3jhd43wy/hg38.gencode_v32.tar.gz",
	'mm10.gencode_vM25' => "https://www.dropbox.com/s/a2397vqfm1igpml/mm10.gencode_vM25.tar.gz",
	'TAIR10.AtRTDv2' => "https://www.dropbox.com/s/kekn3p6e2n5lv88/TAIR10.AtRTDv2.tar.gz",
};
my ($genome) = &readParameters();#->171
my ($scafe_dir, $script_dir, $genome_dir) = &prepDir();#->145
&download($genome_dir, $genome, $genome_url_hsh_ref);#->117
#<\section>
#====================================================================================================================================================#

#====================================================================================================================================================#
#	section 1_run
#
#<section ID="run" num="1">
#<\section>
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#====================================================================================================================================================#
}	#Main sections lexical scope ends
#====================================================================================================================================================#

#====================================================================================================================================================#
#List of subroutines by category
#
#	general [n=1]:
#		readParameters
#
#	unassigned [n=2]:
#		download, prepDir
#
#====================================================================================================================================================#

sub download {
#....................................................................................................................................................#
#	subroutineCategory: unassigned
#	dependOnSub: >none
#	appearInSub: >none
#	primaryAppearInSection: 0_startTasks|79
#	secondaryAppearInSection: >none
#	input: $genome, $genome_dir, $genome_url_hsh_ref
#	output: 
#	toCall: &download($genome_dir, $genome, $genome_url_hsh_ref);
#	calledInLine: 90
#....................................................................................................................................................#
	my ($genome_dir, $genome, $genome_url_hsh_ref) = @_;
	
	my $tar_gz_path = "$genome_dir/$genome.tar.gz";
	my $genome_url = $genome_url_hsh_ref->{$genome};
	
	die "genome $genome is not avaiable\n" if not exists $genome_url_hsh_ref->{$genome};

	print "Cleaning up $genome_dir/$genome/";
	system ("rm -f $tar_gz_path");
	system ("rm -rf $genome_dir/$genome/");
	system ("wget $genome_url -P $genome_dir");
	system ("tar -xzvf $tar_gz_path -C $genome_dir");
	system ("rm $tar_gz_path");

	return ();
}
sub prepDir {
#....................................................................................................................................................#
#	subroutineCategory: unassigned
#	dependOnSub: >none
#	appearInSub: >none
#	primaryAppearInSection: 0_startTasks|79
#	secondaryAppearInSection: >none
#	input: none
#	output: $genome_dir, $scafe_dir, $script_dir
#	toCall: my ($scafe_dir, $script_dir, $genome_dir) = &prepDir();
#	calledInLine: 89
#....................................................................................................................................................#

	my $scriptAbsPath = abs_path($0);
	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 $genome_dir = $scafe_dir."/resources/genome/"; push @mkDirAry, $genome_dir;
	foreach my $dir (@mkDirAry) {system ("mkdir -pm 755 $dir");}

	return ($scafe_dir, $script_dir, $genome_dir);
}
sub readParameters {
#....................................................................................................................................................#
#	subroutineCategory: general
#	dependOnSub: >none
#	appearInSub: >none
#	primaryAppearInSection: 0_startTasks|79
#	secondaryAppearInSection: >none
#	input: none
#	output: $genome
#	toCall: my ($genome) = &readParameters();
#	calledInLine: 88
#....................................................................................................................................................#
	
	my ($genome);
	
	GetOptions 	(
		"genome=s"	=>	\$genome,
		'help'		=>	sub { HelpMessage(0) },
	) or HelpMessage(1);

	HelpMessage(1) unless $genome;

	return($genome);

}

exit;