Matrix Science header

resfile_params.pl

Example program for retrieving search parameter data.

#!/usr/local/bin/perl
##############################################################################
# file: resfile_params.pl                                                    #
# 'msparser' toolkit                                                         #
# Test harness / example code                                                #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2010 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#     $Source: /vol/cvsroot/parser/examples/test_perl/resfile_params.pl,v $ #
#     $Author: villek $ #
#       $Date: 2010/08/31 08:48:07 $ #
#   $Revision: 1.4 $ #
# $NoKeywords::                                                            $ #
##############################################################################
use strict;
##############################################################################

use msparser;

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

my $file = new msparser::ms_mascotresfile($ARGV[0]);

if ($file->isValid) {
    searchParameters($file);
}

##############################################################################
#  searchParameters                                                          #
#  Display parameters from the ms_searchparams object.                       #
#  The values come from the parameters and the masses sections of the file   #
##############################################################################
sub searchParameters {
    my ($resfile) = @_;

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

    print "Search parameters from ms_searchparams"         , "\n";
    print "========================================="      , "\n";
    printf $fmt, "License"             , $params->getLICENSE();
    printf $fmt, "Search title"        , $params->getCOM();
    printf $fmt, "SEG mass"            , $params->getSEG();
    printf $fmt, "Peptide tol"         , $params->getTOL();
    printf $fmt, "Peptide tol units"   , $params->getTOLU();
    printf $fmt, "Fragment tol"        , $params->getITOL();
    printf $fmt, "Fragment tol units"  , $params->getITOLU();
    printf $fmt, "Missed cleavages"    , $params->getPFA();
    printf $fmt, "Database"            , $params->getDB();
    printf $fmt, "Static mods"         , $params->getMODS();
    printf $fmt, "Average/monoisotopic", $params->getMASS();
    printf $fmt, "Enzyme"              , $params->getCLE();
    printf $fmt, "Raw data file name"  , $params->getFILENAME();
    printf $fmt, "Input data"          , $params->getQUE();
    printf $fmt, "Type of search"      , $params->getSEARCH();
    printf $fmt, "User name"           , $params->getUSERNAME();
    printf $fmt, "User email"          , $params->getUSEREMAIL();
    printf $fmt, "Charge state"        , $params->getCHARGE();
    printf $fmt, "Repeat search file"  , $params->getINTERMEDIATE();
    printf $fmt, "Num hits to display" , $params->getREPORT();
    printf $fmt, "Show overview"       , $params->getOVERVIEW();
    printf $fmt, "Data file format"    , $params->getFORMAT();
    printf $fmt, "Form version"        , $params->getFORMVER();
    printf $fmt, "Variable mods"       , $params->getIT_MODS();

    for my $i (0 .. 12) {
        printf $fmt, sprintf("User%02d", $i), $params->getUSERField($i);
    }

    printf $fmt, "Precursor mass"      , $params->getPRECURSOR();
    printf $fmt, "Taxonomy filter"     , $params->getTAXONOMY();
    printf $fmt, "Type of report"      , $params->getREPTYPE();
    printf $fmt, "Accessions to search", $params->getACCESSION();
    printf $fmt, "Subcluster used"     , $params->getSUBCLUSTER();
    printf $fmt, "ICAT search?"        , $params->getICAT();
    printf $fmt, "Instrument type"     , $params->getINSTRUMENT();
    printf $fmt, "Error tolerant?"     , $params->getERRORTOLERANT();
    printf $fmt, "Rules (ions series)" , $params->getRULES();

    for my $ch (ord('A') .. ord('Z')) {
        printf $fmt, join(' ', "Residue", chr($ch)), $params->getResidueMass(chr($ch));
    }

    printf $fmt, "C terminus mass" , $params->getCTermMass();
    printf $fmt, "N terminus mass" , $params->getNTermMass();
    printf $fmt, "Mass of hydrogen", $params->getHydrogenMass();
    printf $fmt, "Mass of oxygen"  , $params->getOxygenMass();
    printf $fmt, "Mass of carbon"  , $params->getCarbonMass();
    printf $fmt, "Mass of nitrogen", $params->getNitrogenMass();
    printf $fmt, "Mass of electron", $params->getElectronMass();

    my $i = 1;
    while ($params->getVarModsName($i)) {
        printf $fmt, "Variable mod name"   , $params->getVarModsName($i);
        printf $fmt, "Variable mod delta"  , $params->getVarModsDelta($i), "\n";
        printf $fmt, "Variable mod neutral", $params->getVarModsNeutralLoss($i), "\n";
        $i++;
    }

    print "\n\n";
}


=pod

Running the program as

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

will give the following output under Mascot Server 2.3:


Search parameters from ms_searchparams
=========================================
License             : Licensed to: Matrix Science Internal use only - Frill, (4 processors).
Search title        : MS/MS Example
SEG mass            : -1
Peptide tol         : 0.2
Peptide tol units   : Da
Fragment tol        : 0.2
Fragment tol units  : Da
Missed cleavages    : 1
Database            : SwissProt
Static mods         : 
Average/monoisotopic: Monoisotopic
Enzyme              : Trypsin
Raw data file name  : C:\Auto MSMS output\Sample 1.pkl
Input data          : 
Type of search      : MIS
User name           : 
User email          : 
Charge state        : 2+
Repeat search file  : ../data/F981123.dat
Num hits to display : 0
Show overview       : 
Data file format    : Mascot generic
Form version        : 1.01
Variable mods       : Oxidation (M)
User00              : 
User01              : 
User02              : 
User03              : 
User04              : 
User05              : 
User06              : 
User07              : 
User08              : 
User09              : 
User10              : 
User11              : 
User12              : 
Precursor mass      : 0
Taxonomy filter     : All entries
Type of report      : Peptide
Accessions to search: 
Subcluster used     : -1
ICAT search?        : 
Instrument type     : ESI-QUAD-TOF
Error tolerant?     : 
Rules (ions series) : 1,2,8,9,10,13,14,15
Residue A           : 71.037114
Residue B           : 114.53494
Residue C           : 103.009185
Residue D           : 115.026943
Residue E           : 129.042593
Residue F           : 147.068414
Residue G           : 57.021464
Residue H           : 137.058912
Residue I           : 113.084064
Residue J           : 0
Residue K           : 128.094963
Residue L           : 113.084064
Residue M           : 131.040485
Residue N           : 114.042927
Residue O           : 0
Residue P           : 97.052764
Residue Q           : 128.058578
Residue R           : 156.101111
Residue S           : 87.032028
Residue T           : 101.047679
Residue U           : 150.95363
Residue V           : 99.068414
Residue W           : 186.079313
Residue X           : 111
Residue Y           : 163.063329
Residue Z           : 128.55059
C terminus mass     : 17.00274
N terminus mass     : 1.007825
Mass of hydrogen    : 1.007825
Mass of oxygen      : 15.994915
Mass of carbon      : 12
Mass of nitrogen    : 14.003074
Mass of electron    : 0.000549
Variable mod name   : Oxidation (M)
Variable mod delta  : 15.994919
Variable mod neutral: 0


=cut

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