BOL: Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !

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Jit
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !

Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !

By Jit 1153 days ago

use strict;
use warnings;
use ExtUtils::Installed;
use LWP::Simple;
use Archive::Extract;
#
# First, check if all the required modules have been installed in the system and download the mandatory database
#
BEGIN {
    my @import_modules = (
    'Cwd',
    'File::chdir',
    'File::Copy',
    'POSIX',
    'Tie::File',
    'Try::Tiny',
    'Data::Dumper',
    'File::Basename',
    'Bio::SeqIO',
    'FindBin',
    'File::Remove',
    'Capture::Tiny',
    'File::Temp',
    'File::Spec::Functions',
    'Statistics::Multtest',
    'File::Path',
    'Statistics::Distributions',
    'Getopt::Long',
    'Statistics::R',
    'Math::Round',
    'File::Find',
    'Bio::DB::Taxonomy',
    'Pod::Usage',
        );

    my ($inst) = ExtUtils::Installed->new();
    my (@installed_modules) = $inst->modules();

    for ( @import_modules ) {

        eval{ $inst->validate($_) };
        if($@) {
            print qq{\n Module $_   NOT OK!\n };
            #exit 1;
        } # end 'if'
        else { print "\n Module $_ OK!\n";}
    } # end 'for'
} # end 'BEGIN' block

#Bash script else here

print "\nDownloading third party database for Alienomics\n";

#Install NCBI taxdump
my $url = 'ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz';
my $file = 'taxdump.tar.gz';

my $code = getstore($url, $file);
#print $code;

my $ae = Archive::Extract->new( archive => $file);

my $ok = $ae->extract( to => 'third_party_DB/taxdump' );


#Install silvaDB
#https://www.arb-silva.de/no_cache/download/archive/release_138_1/Exports/
#LSU: Large subunit (23S/28S ribosomal RNAs)
#SSU: Small subunit (16S/18S ribosomal RNAs)

my $silva_url_LSU = 'https://www.arb-silva.de/fileadmin/silva_databases/release_138_1/Exports/SILVA_138.1_LSUParc_tax_silva.fasta.gz';
my $silva_LSU_fileName = 'SILVA_138.1_LSUParc_tax_silva.fasta.gz';

my $silva_LSU_code = getstore($silva_url_LSU, $silva_LSU_fileName);
#print $silva_LSU_code;

my $silva_LSU_ae = Archive::Extract->new( archive => $silva_LSU_fileName);

my $silva_ok = $silva_LSU_ae->extract( to => 'third_party_DB/silvaDB/SILVA_138.1_LSUParc_tax_silva.fasta' );


#Install buscoDB
#https://busco-archive.ezlab.org/

my $busco_url_LSU = 'https://busco-archive.ezlab.org/datasets/metazoa_odb9.tar.gz';
my $busco_LSU_fileName = 'metazoa_odb9.tar.gz';

my $busco_LSU_code = getstore($busco_url_LSU, $busco_LSU_fileName);
#print $busco_LSU_code;

my $busco_LSU_ae = Archive::Extract->new( archive => $busco_LSU_fileName);

my $busco_ok = $busco_LSU_ae->extract( to => 'third_party_DB/' );


#Install diamondDB


__END__

# BlastDB download
my $result = `mkdir taxdump; cd taxdump; wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz; tar xzfp taxdump.tar.gz`;
parseResult ($result);

#do your magic here
sub parseResult {
  system ($_[0]);
}

__END__
my $content = get("ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz");
die "Couldn't get it!" unless defined $content;

if (is_success(get("$content"))) {
    print "Download started";
}



if [ ! -d "$PWD/blastDB" ]; then
    if [ ! -d "$PWD/blastDB" ]; then
        mkdir $PWD/blastDB
    fi
    cd $PWD/blastDB
    wget "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.*.tar.gz"
    for a in nt.*.tar.gz; do tar xzf $a; done
    #Out of the directory
    cd ..
else
   echo -e "exists \t blastDB, If not installed sucessfully, delete the folder and re-run it"
fi

echo -e "\nAll Done\n"

echo -e "\nInstall R package install.packages('Ckmeans.1d.dp') \n"

/;

BOL

Jit

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Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !