config_enzymes.pl

Read in the enzymes file.

#!/usr/local/bin/perl
##############################################################################
# file: config_enzymes.pl                                                    #
# 'msparser' toolkit example code                                            #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2010 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#     $Source: parser/examples/test_perl/config_enzymes.pl $ #
#     $Author: villek@matrixscience.com $                                                      #
#       $Date: 2018-07-30 16:23:53 +0100 $                                         #
#   $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $                                                         #
# $NoKeywords::                                                            $ #
##############################################################################
use strict;
##############################################################################
 
use msparser;
 
if (!defined($ARGV[0])) {
    print <<EOF;
The location of 'enzymes' file has to be specified as a parameter.
The location should either be the full path to the 'enzymes' file
or a URL to a Mascot server - e.g. http://mascot-server/mascot/cgi
EOF
    exit 1;
}
 
# Note: $cs must not be lexically scoped; you need to keep it in scope
# for as long as you use $file. See "Using the toolkit from Perl, Java and 
# Python" in Mascot Parser manual.
my ($file, $cs);
 
# A sessionID can optionally be passed as the second parameter.
# This will only be required if the 'file' is a URL.
if (defined($ARGV[1])) {
    $cs = new msparser::ms_connection_settings;
    $cs->setSessionID($ARGV[1]);
    $file = new msparser::ms_enzymefile($ARGV[0], $cs);
} else {
    $file = new msparser::ms_enzymefile($ARGV[0]);
}
 
if (!$file->isValid) {
    print "There are errors. Cannot continue. The last error description:\n";
    print $file->getLastErrorString(), "\n";
    exit 1;
}
 
my $n = $file->getNumberOfEnzymes();
print "There are ", $n, " enzyme definitions available\n";
 
for my $i (0 .. $n-1) {
    my $enzyme = $file->getEnzymeByNumber($i);
    print $enzyme->getTitle(), ": ";
 
    for my $c (0 .. $enzyme->getNumberOfCutters - 1) {
        if ($enzyme->getCutterType($c) == $msparser::ms_enzyme::NTERM_CUTTER) {
            print "nTerm - ";
        } else {
            print "cTerm - ";
        }
 
        print $enzyme->getCleave($c), "!", $enzyme->getRestrict($c);
        print "; ";
    }
    print "\n";
}
 
# Now try updating the first one in the list to semi-specific.
my $enzyme = $file->getEnzymeByNumber(0);
$enzyme->setSemiSpecific(1);
$file->updateEnzymeByNumber(0, $enzyme);
 
# And delete V8-DE.
$file->deleteEnzymeByName("V8-DE");
 
# Finally, save the file under a new name.
$file->setFileName($ARGV[0] . ".new");
$file->save_file;
 
if (!$file->isValid) {
    print "Failed to save: ", $file->getLastErrorString, "\n";
} else {
    print $ARGV[0], ".new now has ", $file->getNumberOfEnzymes, " enzyme definitions available\n";
}
 
=pod
 
Running the program as 
 
perl -I../bin config_enzymes.pl ../config/enzymes
 
will give the following output under Mascot Server 2.3: 
 
 
There are 21 enzyme definitions available
Trypsin: cTerm - KR!P; 
Trypsin/P: cTerm - KR!; 
Arg-C: cTerm - R!P; 
Asp-N: nTerm - BD!; 
Asp-N_ambic: nTerm - DE!; 
Chymotrypsin: cTerm - FLWY!P; 
CNBr: cTerm - M!; 
CNBr+Trypsin: cTerm - M!; cTerm - KR!P; 
Formic_acid: nTerm - D!; cTerm - D!; 
Lys-C: cTerm - K!P; 
Lys-C/P: cTerm - K!; 
LysC+AspN: nTerm - BD!; cTerm - K!P; 
Lys-N: nTerm - K!; 
PepsinA: cTerm - FL!; 
semiTrypsin: cTerm - KR!P; 
TrypChymo: cTerm - FKLRWY!P; 
TrypsinMSIPI: nTerm - J!; cTerm - KR!P; cTerm - J!; 
TrypsinMSIPI/P: nTerm - J!; cTerm - JKR!; 
V8-DE: cTerm - BDEZ!P; 
V8-E: cTerm - EZ!P; 
None: cTerm - KR!P; 
../config/enzymes.new now has 20 enzyme definitions available
 
 
=cut