Hi guys,

I am currently writing a perl script which compares two directories containing fasta files. The first contains all fasta sequences grouped by their location on the chromosomes. The second directory contains fasta consensus sequences taken from each file of the first directory. What I want is to get in the same file:

• Name of each consensus name (LOC126... for example)
• Length of each consensus sequence
• Name of each CDS used to make one consensus sequence (XM... for example)
• Length of each CDS.

I have written a code which works well. The bad side is that it takes two much time to execute. My question is: Is there any way to accelerate its execution ? i have several loops in my script and since I am new to perl I suppose that maybe i am not using the more accurate solution.

Thank you !

My code is above:

#!/usr/local/perl-5.24.0/bin/perl 
 if (scalar @ARGV < 2)
{ 
    print " Number or arguments not sufficient, please read the usage !\n\n
            Usage : perl FilterConsensus.pl  -d LOCfilesDirectory -c ConsensusDirectory\n\n
            ************************** Mandatory arguments: ****************************\n\n
            -d Complete path to your LOCfiles that contains your different CDS per LOCATION (exemple: -d home/your_username/Data/LOCFILES)\n\n
            -c Complete path to your CONSENSUS files.  (exemple: -c home/your_username/Data/CONSENSUS)\n\n
            ***************************************************************************************************\n\n";
    exit;
}
my ($locdir, $consdir);
GetOptions( "d|repertoire=s"=>\$locdir,
            "c|consensus=s"=>\$consdir);
my $master_dir = "/home/andiaye/Data/EPIALTER/Données/RESUME";
mkdir $master_dir, 0755; 
my @consfiles = GetFilesList($consdir);
my @locfiles = GetFilesList($locdir);
my (%hashIDLength, $consfilename, $locfilename, $consID, $conslength);
my $resumefile = "$master_dir/resume.txt";
open my $fic ,'>', $resumefile or die "Cannot open $resumefile\n";
foreach my $consfile(@consfiles){
    $consfilename = Getfilename($consfile);
    ($consID, $conslength)=GetConsIDLength($consfile);
    foreach my $locfile(@locfiles){
        $locfilename = Getfilename($locfile);
        %hashIDLength = GetLocIDLength($locfile);
        while ((my $key, my $value)=each %hashIDLength){
            if ($consfilename=~$locfilename){   
            printf $fic ("%20s %20s %30s %20s\n", "Locus: $consID","Taille Locus: $conslength","CDS:$key", "Taille CDS:$value");
            }
        }
    }
}
close($fic);

#~~~~~~~~~~~~~Functions~~~~~~~~~~~~~#
sub GetFilesList{
        my $Path = $_[0];
        my $FileFound;
        my @FilesList=();
        opendir (my $FhRep, $Path) or die "Can't open directory $Path\n";
        my @Contenu = grep { !/^\.\.?$/ } readdir($FhRep);
        closedir ($FhRep);

        foreach my $FileFound (@Contenu) {
                if ( -f "$Path/$FileFound") {
                        push ( @FilesList, "$Path/$FileFound" );
                }
                elsif ( -d "$Path/$FileFound") {
                        push (@FilesList, GetFilesList("$Path/$FileFound"));
                }
        }
return @FilesList;
}

sub GetConsIDLength {
    my $file = shift @_;
    my ($ID, $length);
    open my $fic ,'<', $file or die "Cannot open $file\n";
    while (my $line = <$fic>){
        chomp $line;
        if ($line =~ m/^>/){
            $ID = (split(m/>/,$line))[1];
            next;
        } 
        else {
            $length += length($line);
        }
    }
    return ($ID, $length); 
    close($fic);
}

sub GetLocIDLength {
    my $file = shift @_;
    my ($ID, $length);
    my %hashIDLength;
    open my $fic ,'<', $file or die "Cannot open $file\n";
    while (my $line = <$fic>){
        chomp $line;
        if ($line =~ m/^>/){
            my @attributs = split(m/ /,$line);
            my $IDsign = $attributs[0];
            $ID = (split(m/>/,$IDsign))[1];
            next;
        } 
        else {
            $length += length($line);
        }
        $hashIDLength{$ID} = $length;
    }
    return (%hashIDLength); 
    close($fic);
}

sub Getfilename {
    my $path = shift @_;
    my($base, $pathe, $ext) = fileparse("$path", '\..*');
    return $base;
}
exit;