Kinetic parser.pl

#!/usr/bin/perl

# Program to parse kinetic data produced by the plate reader at Couchin lab.
# The data structure is not complicated, but almost impossible to extract data manually:
# one line contains all data for the 96 wells in each time step.
# What the program does is to collect the absorbance value correspondig to each well for each timestep and makes a table


# Usage:
# $./Kinetic_parser.pl <Infile> >Outfile

# (c) Daniel Suveges

# v 1.0 2011.09.30
    # Very primitive form, but works anyway

# v 2.0 2011.10.04
    # Trained to get all possible 96 well data, but returns only those that actually filled
    # Cleaning input data is not required

# v 2.5 2013.06.28
    # An error is fixed: real labeling of the wells.
    # Deals with multiple experiments!!!
    # Time format is in minutes with decimal values instead of the min:sec format

our $version    = "2.5";

use strict;
use warnings;


my @lines       = ();
our %AllData    = ();
my @time        = ();

# REadin the files line by line
foreach (<>){
    # A line can be separeted by \r or \n
    push(@lines,split(/[\r\n+]/,$_));
}

my $lineNo  = "";
my $time    = "";

foreach my $line (@lines){
    # print "$line!!\n";
    # my $time    = "";
    if ($line =~ /(\d+\:\d+)\t([\d\.]+)([\d\.\t]+)/){
        $lineNo = "0";
        &row($lineNo,$3);

        my ($min, $sec) = split(/:/,$1);
        $time    = $min + (int($sec / 0.6)/100);
        push (@time, $time);
    }
    elsif ($line =~ /^\t([\d\t\.]+\d)/){
        $lineNo ++;
        &row($lineNo,$1);
    }
    else {
        next;
    }

}

print "Time\t";
my @keys    = keys %AllData;
foreach my $keys (@keys){
    print "$keys\t"
}
print "\n";

for ( my $i = 0; $i < scalar @{$AllData{$keys[0]}}; $i++){
    print "$time[$i]\t";
    foreach my $keys (keys %AllData){
        print "${$AllData{$keys}}[$i]\t";

    }
    print "\n";

}

# parsing a row of the outputfile
sub row {
    my $LineNo  = $_[0];
    my $line    = $_[1];

    my @stuff   = split(/\t/, $line);
    my @letters = qw(A B C D E F G H);

    # Reading all lines. Every line is a timestep with data correspondig to all 96 well
    for( my $index = "0"; $index <= scalar (@stuff); $index++){

        # If the element is exists, let's see which well is it?.
        if($stuff[$index]){

            #Find the position in the plate
              # Find the row (A-H)
              my $row = $letters[int($index/12)];
              # Find the column (1-12)
              my $column = $index % 12;

            push(@{$AllData{$row.$column}},$stuff[$index]);
        }
    }
}