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: parser/examples/test_perl/resfile_params.pl $ #
# $Author: villek@matrixscience.com $ #
# $Date: 2018-07-30 16:23:53 +0100 $ #
# $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $ #
# $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
