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#!/usr/bin/perl -w
#*******************************************************************************
# multi.pl *
# Copyright (C) Nicolas Le Novre and Marine Dumousseau 2009 *
# Run the program melting on several nucleic acid sequences entered from stdin *
# (it can be a file redirected with 'multi.pl < file.seq') *
#*******************************************************************************/
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# Nicolas Le Novre and Marine Dumousseau
# EMBL-EBI, Wellcome-Trust Genome Campus
# Hinxton Cambridge, CB10 1SD, UK
# lenov@ebi.ac.uk
###################################################################
# Usage is: ./multi.pl config_file < inputfile > outputfile #
# Where inputfile contains one sequence per line. No space before #
# sequence and at least one space before extra information #
# Write the parameters of melting in an input file. See manual. #
###################################################################
use strict;
my @linecontent; # contains the elements of a line generated by the function split
my $infile; # contains the parameters of the run except the sequence
my @sequences; # contains all the sequences from which to predict the Tm
my $seq; # one sequence
my @rawresults; # contains the raw output of MELTING
my ($tm,$H,$S);
if (not defined $ARGV[0]){
print "Except the sequences, all parameters have to be contained in a \n",
"configuration file, and the script run as:\n",
" prompt> ./multi.pl config_file < inputfile > outputfile\n";
exit;
}
# Read the sequences to analise
while (<STDIN>){
if ( $_ !~ /^(\s*\#.*|\s+)$/){ # do not take into account comment and blank lines
chomp;
@linecontent = split(" "); # Note that each line could contain
push(@sequences,$linecontent[0]); # other elements used in derived programs
}
}
print "sequences DeltaH DeltaS Tm (deg C) \n";
foreach $seq (@sequences){
@rawresults = `melting -I$ARGV[0] -S$seq -q`;
foreach (@rawresults){
@linecontent = split(" ");
if ($linecontent[0] =~ /melting/i ){ $tm = $linecontent[2];
} elsif ($linecontent[0] =~ /enthalpy/i ){ $H = $linecontent[1];
} elsif ($linecontent[0] =~ /entropy/i ){ $S = $linecontent[1];
}
}
printf "%-30s %6.0f %5.1f %4.1f\n",$seq, $H, $S, $tm;
}
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