Gcluster/test.pl at master · Xiangyang1984/Gcluster · GitHub

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#!usr/bin/perl -w

use strict;
use warnings;
use FindBin;

###Test-step1: Checks for Gcluster dependencies
print "\n\nTest-step1: Checks for Gcluster dependencies...\n";
print "################################################################\n";
#Checks for perl modules
&check_perl_modules;
print "\n----------------------------------------------------------------\n";
#Chechs for programs
&check_programs;
print "################################################################\n";


my $script_dir = $FindBin::Bin;


###Test-step2: Begin test Gcluster.pl with the test_data
print "\n\n\n\n\nTest-step2: Begin test Gcluster.pl...\n";
print "################################################################\n";
my $check_g = system ("perl $script_dir/Gcluster.pl -dir $script_dir/test_data/gbk -gene $script_dir/test_data/interested_gene_name.txt -tree $script_dir/test_data/16S_rRNA_tree.nwk -m 4");
print "################################################################\n";
if ($check_g eq 0){
    print "Ok, Gcluster.pl works success!\n\n";
}else {
    print "Not Ok, Gcluster.pl works with some errors!\n\n";
}

##########160 genomes data are used to create the compact version of the image in Fig. 1
# This command is used to create the compact version of the image in Fig. 1 in the manuscript using 160 genomes datas, which can be download from http://www.microbialgenomic.com/160_genomes_testdata.tar.gz.
# (1) first run Gcluster: $check_g = system ("perl $script_dir/Gcluster.pl -dir $script_dir/160_genomes_testdata/160_gbk -gene $script_dir/160_genomes_testdata/interested_gene_name.txt -tree $script_dir/160_genomes_testdata/160.rRNA.nwk -m 10 -n 10 -size 1 -dis 5 -l 1 -w 1 -PNG T -strain_name_font_size 3 -scale 0.15 -x_step 1 -dw 0.2");
# (2) modified the genes' names by editing the sub_TFT files
# (3) run Gcluser again with the same options as step (1), and add an option "-map T": my $check_g = system ("perl $script_dir/Gcluster.pl -dir $script_dir/160_genomes_testdata/160_gbk -gene $script_dir/160_genomes_testdata/interested_gene_name.txt -tree $script_dir/160_genomes_testdata/160.rRNA.nwk -m 10 -n 10 -size 1 -dis 5 -l 1 -w 1 -PNG T -map T -strain_name_font_size 3 -scale 0.15 -x_step 1 -dw 0.2");
#########


###Test-step3: Begin test interested_gene_generation.pl with the test_data
print "\n\n\n\n\nTest-step3: Begin test interested_gene_generation.pl...\n";
print "################################################################\n";
my $check_i = system ("perl $script_dir/interested_gene_generation.pl -dir $script_dir/test_data/gbk -db $script_dir/test_data/aioB.fasta -m 4");
print "################################################################\n";
if ($check_i eq 0){
    print "Ok, interested_gene_generation.pl works success!\n\n";
}else {
    print "Not Ok, interested_gene_generation.pl works with some errors!\n\n";
}


#check Perl modules dependencies;
sub check_perl_modules {

    my @test_modules = ("GD", "GD::SVG", "SVG", "threads", "File::Basename", "FindBin", "lib", "Getopt::Long", "Math::BigFloat", "Storable", "vars", "File::Spec", "Bio::SeqIO", "Bio::Tree::NodeI", "Bio::TreeIO");

    my $check_number=0;
    foreach (@test_modules){
        my $cmd = "perl -M$_ -e 'print \"***$_ Version\\t \".$_->VERSION.\"\tok.\n\"'";
        #perl -MGD::SVG -e 'print GD::SVG->VERSION. "\n"'
        my $test_out = system ($cmd);

        print  "***Warning:\t$_ is not installed\n" if $test_out ne 0;
        $check_number++ if $test_out ne 0;
    }
    if ($check_number == 0){
        print "!!!Ok, all dependencies Perl modulers are installed*\n";
    }else{
        print "!!!Not ok, it appears that certain dependencies Perl modulers are installed*\n";
    }
}


# checks software dependencies
sub check_programs{

    print "Checking for makeblastdb ... ";
    my $makeblastdb_path = `which makeblastdb`;
    chomp $makeblastdb_path;
    if (not -e $makeblastdb_path){
    	print "error: makeblastdb is not installed\n";
    }
    else{
	    print "OK, makeblastdb is installed at: $makeblastdb_path\n";
    }

    print "Checking for blastp ... ";
    my $blastp_path = `which blastp`;
    chomp $blastp_path;
    if (not -e $blastp_path){
    	print "error: blastp is not installed\n";
    }
    else{
    	print "OK, blastp is installed at: $blastp_path\n";
    }

    print "Checking for mcl ... ";
    my $mcl_path = `which mcl`;
    chomp $mcl_path;
    if (not -e $mcl_path){
    	print "error: mcl is not installed\n";
    }
    else{
	    print "OK, mcl is installed at: $mcl_path\n";
    }

}