msparser/help/resfile_info_8pl-example.html

#!/usr/local/bin/perl

##############################################################################

# file: resfile_info.pl                                                      #

# 'msparser' toolkit                                                         #

# Test harness / example code                                                #

##############################################################################

# COPYRIGHT NOTICE                                                           #

# Copyright 1998-2010 Matrix Science Limited  All Rights Reserved.           #

#                                                                            #

##############################################################################

#     $Source: parser/examples/test_perl/resfile_info.pl $ #

#     $Author: robertog@matrixscience.com $ #

#       $Date: 2024-09-04 10:23:46 +0100 $ #

#   $Revision: 526921a73137894bb1eae0b0fc8ccb4bb52ea662 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $ #

# $NoKeywords::                                                            $ #

##############################################################################

use strict;

##############################################################################


use msparser;


if (!defined($ARGV[0])) { die "Must specify results filename as parameter"; }


my $file = msparser::ms_mascotresfilebase::createResfile($ARGV[0]);


if ($file->isValid) {

    searchInformation($file);

}


##############################################################################

#  searchInformation                                                         #

#  - parameter 0  ms_mascotresfilebase                                       #

#  Display parameters from the ms_mascotresfilebase object. The functions        #

#  anyPMF, anyMSMS, anySQ should normally be used in preference to isPMF etc #

#  because some people submit MSMS though the sequence query window etc.     #

##############################################################################

sub searchInformation {

    my ($resfile) = @_;


    my $fmt = "%-20s: %s\n";


    print "Search information from ms_mascotresfilebase", "\n";

    print "========================================", "\n";

    printf $fmt, "Number of queries"   , $resfile->getNumQueries();

    printf $fmt, "Number of sequences" , $resfile->getNumSeqs();

    printf $fmt, "Sequences after tax" , $resfile->getNumSeqsAfterTax();

    printf $fmt, "Number of residues"  , $resfile->getNumResidues();

    printf $fmt, "Execution time"      , $resfile->getExecTime();

    printf $fmt, "Date (seconds)"      , $resfile->getDate();


    # Let's jump through a few hoops to get the equivalent of a 'C' asctime call

    my ($sec, $min, $hour, $mday, $mon, $year, $wday, $yday, $isdst)

        = localtime($resfile->getDate);


    printf $fmt, "Date", sprintf("%s %s %d %02d:%02d:%02d %d",

        (qw(Sun Mon Tue Wed Thu Fri Sat))[$wday],

        (qw(Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec))[$mon],

        $mday,

        $hour,

        $min,

        $sec,

        $year+1900

    );


    printf $fmt, "Mascot version"       , $resfile->getMascotVer();

    printf $fmt, "Fasta version"        , $resfile->getFastaVer();

    printf $fmt, "Is PMF?"              , $resfile->isPMF();

    printf $fmt, "Is MSMS?"             , $resfile->isMSMS();

    printf $fmt, "Is SQ?"               , $resfile->isSQ();

    printf $fmt, "Is Error tolerant"    , $resfile->isErrorTolerant();

    printf $fmt, "Any PMF?"             , $resfile->anyPMF();

    printf $fmt, "Any MSMS?"            , $resfile->anyMSMS();

    printf $fmt, "Any SQ?"              , $resfile->anySQ();

    printf $fmt, "Any peptide matches"  , $resfile->anyFastaMatches();


    print "\n";

}


=pod


Running the program as


perl -I../bin resfile_info.pl ../data/F981123.dat


will give the following output under Mascot Server 2.3


Search information from ms_mascotresfilebase

========================================

Number of queries   : 67

Number of hits      : 50

Number of sequences : 257964

Sequences after tax : 257964

Number of residues  : 93947433

Execution time      : 6

Date (seconds)      : 1171894187

Date                : Mon Feb 19 14:09:47 2007

Mascot version      : 2.1.119

Fasta version       : SwissProt_51.6.fasta

Is PMF?             :

Is MSMS?            : 1

Is SQ?              :

Is Error tolerant   :

Any PMF?            :

Any MSMS?           : 1

Any SQ?             :

Any peptide matches : 1


=cut