Perl Parser To Extract Data From Pdb Files

Question

[johnprakash063]

I need this loop to run a directory with many .pdb files. So far it works but the problem is the values of $parsedData{$line} keep stacking up from the first file to the last, meaning the size of the files keep increasing, and the values are false. The rest of the values(count++) are all running correctly. How can I solve this problem please? Any ideas?

Thank you!

# coordExtract.pl
#     # parser that allows editing a pdb
# file to extract the coordinates

my @pdbFiles = glob("*.pdb");

foreach my $pdbFile (@pdbFiles){

    #count for all amino acids existing in the protein
    $count_of_alanine=0;
    $count_of_arginine=0;  
    $count_of_asparagine=0;
    $count_of_aspartic_acid=0;
    $count_of_cysteine=0;
    $count_of_glutamic_acid=0;
    $count_of_glutamine=0;
    $count_of_glycine=0;
    $count_of_histidine=0;
    $count_of_isoleucine=0;
    $count_of_leucine=0;
    $count_of_lysine=0;
    $count_of_methionine=0; 
    $count_of_phenylalanine=0;
    $count_of_proline=0;
    $count_of_serine=0;
    $count_of_threonine=0;
    $count_of_tryptophan=0;
    $count_of_tyrosine=0;
    $count_of_valine=0;
    #count for all amino acids which hav z coordinate between -15 and 15
    $count_of_alanine2=0;
    $count_of_arginine2=0;
    $count_of_asparagine2=0;
    $count_of_aspartic_acid2=0;
    $count_of_cysteine2=0;
    $count_of_glutamic_acid2=0;
    $count_of_glutamine2=0;
    $count_of_glycine2=0;
    $count_of_histidine2=0;
    $count_of_isoleucine2=0;
    $count_of_leucine2=0;
    $count_of_lysine2=0;
    $count_of_methionine2=0;
    $count_of_phenylalanine2=0;
    $count_of_proline2=0;
    $count_of_serine2=0;
    $count_of_threonine2=0;
    $count_of_tryptophan2=0;
    $count_of_tyrosine2=0;
    $count_of_valine2=0;
    #count for groups of amino acids
    $count_of_charged=0;
    $count_of_polar=0;
    $count_of_aromatic=0;
    $count_of_hydrophobic=0;
    $count_of_charged2=0;
    $count_of_polar2=0;
    $count_of_aromatic2=0;
    $count_of_hydrophobic2=0;


    unless (open(INPUTFILE, $pdbFile)) {
        print "Cannot read from '$pdbFile'.\nProgram closing.\n";
        <STDIN>;
        #exit;
    }

    # load the file into an array
    chomp(@dataArray = <INPUTFILE>);

    # close the file
    close(INPUTFILE);


    ###############
    # LET'S WORK! #
    ###############

    # parse the input file saving only backbone atoms coordinates
    # format: [string "ATOM"] [number] [atom] [aa] whateva [3 decimal numbers] whateva with two dots in between
    for ($line = 0; $line < scalar @dataArray; $line++) {
        if ($dataArray[$line]=~/^HEADER\s+(.*?)$/) {
            $header = $1;
        }
        if ($dataArray[$line]=~/^TITLE\s+(.*?)$/) {
            $parsing{$line} = $1;
        }
        if ($dataArray[$line] =~ m/ATOM\s+(\d+)\s+(\w+)\s+(\w{3})\s+.+\s+(\S+\.\S+)\s+(\S+\.\S+)\s+(\S+\.\S+)\s+.+\..+\..+/ig) {
            if (($2 eq "N" || $2 eq "CA" || $2 eq "C") && ($6 >= -15 && $6 <= 15) && (($3 eq "ARG") || ($3 eq "ASP") || ($3 eq "GLU") || ($3 eq "LYS"))) {
                $parsedData7{$line} = $1."\t\t".$3."\t\t".$4."\t\t".$5."\t\t".$6;
            }

            if ($2 eq "N" || $2 eq "CA" || $2 eq "C") {
                $parsedData{$line} = $1."\t\t".$3."\t\t".$4."\t\t".$5."\t\t".$6;

                if($3 eq "ALA"){
                    $count_of_alanine++;
                }
                if($3 eq "ARG"){
                    $count_of_arginine++;
                }
                if($3 eq "ASN"){
                    $count_of_asparagine++;
                }
                if($3 eq "ASP"){
                    $count_of_aspartic_acid++;
                }
                if($3 eq "CYS"){
                    $count_of_cysteine++;
                }
                if($3 eq "GLU"){
                    $count_of_glutamic_acid++;
                }
                if($3 eq "GLN"){
                    $count_of_glutamine++;
                }
                if($3 eq "GLY"){
                    $count_of_glycine++;
                }
                if($3 eq "HIS"){
                    $count_of_histidine++;
                }
                if($3 eq "ILE"){
                    $count_of_isoleucine++;
                }
                if($3 eq "LEU"){
                    $count_of_leucine++;
                }
                if($3 eq "LYS"){
                    $count_of_lysine++;
                }
                if($3 eq "MET"){
                    $count_of_methionine++;
                }
                if($3 eq "PHE"){
                    $count_of_phenylalanine++;
                }
                if($3 eq "PRO"){
                    $count_of_proline++;
                }
                if($3 eq "SER"){
                    $count_of_serine++;
                }
                if($3 eq "THR"){
                    $count_of_threonine++;
                }
                if($3 eq "TRP"){
                    $count_of_tryptophan++;
                }
                if($3 eq "TYR"){
                    $count_of_tyrosine++;
                }
                if($3 eq "VAL"){
                    $count_of_valine++;
                }
                if($3 eq "ARG"||$3 eq "ASP"||$3 eq "GLU"||$3 eq "LYS"){
                    $count_of_charged++;
                }
                if($3 eq "ASN"||$3 eq "GLN"||$3 eq "GLY"||$3 eq "MET"||$3 eq "PRO"){
                    $count_of_polar++;
                }
                if($3 eq "PHE"||$3 eq "TRP"||$3 eq "TYR"||$3 eq "HIS"){
                    $count_of_aromatic++;
                }
                if($3 eq "ALA"||$3 eq "ILE"||$3 eq "LEU"||$3 eq "VAL"){
                    $count_of_hydrophobic++;
                }
            }
            if (($2 eq "N" || $2 eq "CA" || $2 eq "C") && ($6 >= -15 && $6 <= 15)) {
                $parsedData2{$line} = $1."\t\t".$3."\t\t".$4."\t\t".$5."\t\t".$6;

                if($3 eq "ALA"){
                    $count_of_alanine2++;
                }
                if($3 eq "ARG"){
                    $count_of_arginine2++;
                }
                if($3 eq "ASN"){
                    $count_of_asparagine2++;
                }
                if($3 eq "ASP"){
                    $count_of_aspartic_acid2++;
                }
                if($3 eq "CYS"){
                    $count_of_cysteine2++;
                }
                if($3 eq "GLU"){
                    $count_of_glutamic_acid2++;
                }
                if($3 eq "GLN"){
                    $count_of_glutamine2++;
                }
                if($3 eq "GLY"){
                    $count_of_glycine2++;
                }
                if($3 eq "HIS"){
                    $count_of_histidine2++;
                }
                if($3 eq "ILE"){
                    $count_of_isoleucine2++;
                }
                if($3 eq "LEU"){
                    $count_of_leucine2++;
                }
                if($3 eq "LYS"){
                    $count_of_lysine2++;
                }
                if($3 eq "MET"){
                    $count_of_methionine2++;
                }
                if($3 eq "PHE"){
                    $count_of_phenylalanine2++;
                }
                if($3 eq "PRO"){
                    $count_of_proline2++;
                }
                if($3 eq "SER"){
                    $count_of_serine2++;
                }
                if($3 eq "THR"){
                    $count_of_threonine2++;
                }
                if($3 eq "TRP"){
                    $count_of_tryptophan2++;
                }
                if($3 eq "TYR"){
                    $count_of_tyrosine2++;
                }
                if($3 eq "VAL"){
                    $count_of_valine2++;
                }
                if($3 eq "ARG"||$3 eq "ASP"||$3 eq "GLU"||$3 eq "LYS"){
                    $count_of_charged2++;
                }
                if($3 eq "ASN"||$3 eq "GLN"||$3 eq "GLY"||$3 eq "MET"||$3 eq "PRO"){
                    $count_of_polar2++;
                }
                if($3 eq "PHE"||$3 eq "TRP"||$3 eq "TYR"||$3 eq "HIS"){
                    $count_of_aromatic2++;
                }
                if($3 eq "ALA"||$3 eq "ILE"||$3 eq "LEU"||$3 eq "VAL"){
                    $count_of_hydrophobic2++;
                }
            }
        }
    }

    # create the output file name
    $outputFile = "coordinates_".$pdbFile;

    # open the output file
    open (OUTFILE, ">$outputFile");

    # print the data lines
    print OUTFILE $header, "\n";
    foreach $line (sort {$a <=> $b} keys %parsing) {
        print OUTFILE $parsing{$line}."\n";
    }

    print OUTFILE $title, "\n";
    print OUTFILE "-----------------------------------------------------------------------\n";
    print OUTFILE "------------ALL BACKBONE AMINO ACIDS IN THE MEMBRANE PROTEIN-----------\n";
    print OUTFILE "-----------------------------------------------------------------------\n";
    print OUTFILE "\n";        
    print OUTFILE "Atom Number\tAmino acid\tX coordinate\tY Coordinate\tZ Coordinate\n";

    foreach $line (sort {$a <=> $b} keys %parsedData) {
        print OUTFILE $parsedData{$line}."\n";
    }

    print OUTFILE "\n";
    print OUTFILE "\n";
    print OUTFILE "-----------------------------------------------------------------------\n";
    print OUTFILE "------------ALL AMINO ACIDS WITH Z COORDINATE > -15 && < 15------------\n";
    print OUTFILE "-----------------------------------------------------------------------\n";
    print OUTFILE "\n";    
    print OUTFILE "Atom Number\tAmino acid\tX coordinate\tY Coordinate\tZ Coordinate\n";

    foreach $line (sort {$a <=> $b} keys %parsedData2) {
        print OUTFILE $parsedData2{$line}."\n";
    }   

    print OUTFILE "\n";
    print OUTFILE "\n";
    print OUTFILE "-----------------------------------------------------------------------\n";
    print OUTFILE "------------ALL Charged AMINO ACIDS WITH Z COORDINATE > -15 && < 15------------\n";
    print OUTFILE "-----------------------------------------------------------------------\n";
    print OUTFILE "\n";    
    print OUTFILE "Atom Number\tAmino acid\tX coordinate\tY Coordinate\tZ Coordinate\n";

    foreach $line (sort {$a <=> $b} keys %parsedData7) {
        print OUTFILE $parsedData7{$line}."\n";
    }   

    print OUTFILE "\n";
    print OUTFILE "\n";
    print OUTFILE "------------------------------------------------------------------------\n";
    print OUTFILE "-----AMINO ACID NUMBERS AND PERCENTAGE FOR THE BACKBONE AMINO ACIDS-----\n";
    print OUTFILE "------------------------------------------------------------------------\n";
    print OUTFILE "\n";    
    print OUTFILE "Amino acid\tTotal Number(N)\n";
    print OUTFILE "--------------------------------------------------\n";
    print OUTFILE "Alanine\t\t", $count_of_alanine, "\t\t\n";
    print OUTFILE "Arginine\t", $count_of_arginine, "\t\t\n";
    print OUTFILE "Asparagine\t", $count_of_asparagine, "\t\t\n";
    print OUTFILE "Aspartic Acid\t", $count_of_aspartic_acid, "\t\t\n";
    print OUTFILE "Cysteine\t", $count_of_cysteine, "\t\t\n";
    print OUTFILE "Glutamic Acid\t",$count_of_glutamic_acid, "\t\t\n";
    print OUTFILE "Glutamine\t",$count_of_glutamine, "\t\t\n";
    print OUTFILE "Glycine\t\t",$count_of_glycine, "\t\t\n";
    print OUTFILE "Histidine\t",$count_of_histidine, "\t\t\n";
    print OUTFILE "Isoleucine\t",$count_of_isoleucine, "\t\t\n";
    print OUTFILE "Leucine\t\t",$count_of_leucine, "\t\t\n";
    print OUTFILE "Lysine\t\t",$count_of_lysine, "\t\t\n";
    print OUTFILE "Methionine\t",$count_of_methionine, "\t\t\n";
    print OUTFILE "Phenylalanine\t",$count_of_phenylalanine, "\t\t\n";
    print OUTFILE "Proline\t\t",$count_of_proline, "\t\t\n";
    print OUTFILE "Serine\t\t",$count_of_serine, "\t\t\n";
    print OUTFILE "Threonine\t",$count_of_threonine, "\t\t\n";
    print OUTFILE "Tryptophan\t",$count_of_tryptophan, "\t\t\n";
    print OUTFILE "Tyrosine\t",$count_of_tyrosine, "\t\t\n";
    print OUTFILE "Valine\t\t",$count_of_valine, "\t\t\n";
    print OUTFILE "--------------------------------------------------\n";
    print OUTFILE "Total\t\t", scalar(keys %parsedData), "\t\t\n";
    print OUTFILE "\n";
    print OUTFILE "\n";
    print OUTFILE "CHARGED AMINO ACIDS\t\t\t",$count_of_charged,"\n";
    print OUTFILE "POLAR AMINO ACIDS\t\t\t",$count_of_polar,"\n";
    print OUTFILE "AROMATIC AMINO ACIDS\t\t\t",$count_of_aromatic,"\n";
    print OUTFILE "HYDROPHOBIC AMINO ACIDS\t\t\t",$count_of_hydrophobic,"\n";
    print OUTFILE "\n";
    print OUTFILE "\n";
    print OUTFILE "------------------------------------------------------------------------\n";
    print OUTFILE "----AMINO ACID NUMBERS AND PERCENTAGE FOR Z COORDINATE > -15 && < 15----\n";
    print OUTFILE "------------------------------------------------------------------------\n";
    print OUTFILE "\n";    
    print OUTFILE "Amino acid\tTotal Number(N)\n";
    print OUTFILE "--------------------------------------------------\n";
    print OUTFILE "Alanine\t\t", $count_of_alanine2, "\t\t\n";
    print OUTFILE "Arginine\t", $count_of_arginine2, "\t\t\n";
    print OUTFILE "Asparagine\t", $count_of_asparagine2, "\t\t\n";
    print OUTFILE "Aspartic Acid\t", $count_of_aspartic_acid2, "\t\t\n";
    print OUTFILE "Cysteine\t", $count_of_cysteine2, "\t\t\n";
    print OUTFILE "Glutamic Acid\t",$count_of_glutamic_acid2, "\t\t\n";
    print OUTFILE "Glutamine\t",$count_of_glutamine2, "\t\t\n";
    print OUTFILE "Glycine\t\t",$count_of_glycine2, "\t\t\n";
    print OUTFILE "Histidine\t",$count_of_histidine2, "\t\t\n";
    print OUTFILE "Isoleucine\t",$count_of_isoleucine2, "\t\t\n";
    print OUTFILE "Leucine\t\t",$count_of_leucine2, "\t\t\n";
    print OUTFILE "Lysine\t\t",$count_of_lysine2, "\t\t\n";
    print OUTFILE "Methionine\t",$count_of_methionine2, "\t\t\n";
    print OUTFILE "Phenylalanine\t",$count_of_phenylalanine2, "\t\t\n";
    print OUTFILE "Proline\t\t",$count_of_proline2, "\t\t\n";
    print OUTFILE "Serine\t\t",$count_of_serine2, "\t\t\n";
    print OUTFILE "Threonine\t",$count_of_threonine2, "\t\t\n";
    print OUTFILE "Tryptophan\t",$count_of_tryptophan2, "\t\t\n";
    print OUTFILE "Tyrosine\t",$count_of_tyrosine2, "\t\t\n";
    print OUTFILE "Valine\t\t",$count_of_valine2, "\t\t\n";
    print OUTFILE "--------------------------------------------------\n";
    print OUTFILE "Total\t\t", scalar(keys %parsedData2), "\t\t\n";
    print OUTFILE "\n";
    print OUTFILE "\n";
    print OUTFILE "CHARGED AMINO ACIDS\t\t\t",$count_of_charged2,"\n";
    print OUTFILE "POLAR AMINO ACIDS\t\t\t",$count_of_polar2,"\n";
    print OUTFILE "AROMATIC AMINO ACIDS\t\t\t",$count_of_aromatic2,"\n";
    print OUTFILE "HYDROPHOBIC AMINO ACIDS\t\t\t",$count_of_hydrophobic2,"\n";
    print OUTFILE "\n";
    print OUTFILE "\n";
    print OUTFILE "------------------------------------------------------------------\n";
    print OUTFILE "------------------------------------------------------------------\n";

    # close the output file
    close (OUTFILE);

    # end message
    print "The coordinates of '$pdbFile' were saved into '$outputFile'.\n";
}
# end the program
exit;

Answer 1

[Matt Shirley]

I would start by simplifying your script to make it operate on only one file at a time, produce one output file for each input file, and then use a bash loop to run it on the directory of files. Unless this is a homework assignment where the instructor has given you an assignment to match patterns using if/else while reading all files form a directory in a loop. If you can use it, I also suggest the Bio::Perl pdb parser to do the IO.

[johnprakash063]

actually the bash works for mac platform, but now m working mainly on windows platform, dats the problem actually... and yes, the file does actually read one by one, dats d original file i did, i juz added the loop recently...