msparser/help/resfile_params_8pl-example.html

#!/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: parser/examples/test_perl/resfile_params.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) {

    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