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resfile_info.py

Example program for retrieving general search information.

#!/usr/bin/python
##############################################################################
# file: resfile_info.py                                                      #
# 'msparser' toolkit                                                         #
# Test harness / example code                                                #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2010 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#     $Source: /vol/cvsroot/parser/examples/test_python/resfile_info.py,v $ #
#     $Author: neilr $ #
#       $Date: 2016/03/18 16:23:01 $ #
#   $Revision: 1.3 $ #
# $NoKeywords::                                                            $ #
##############################################################################

import sys
import time
import msparser

def main() :
    if len(sys.argv) < 2 :  
        print("Must specify results filename as parameter")
        return 1

    file = msparser.ms_mascotresfile(sys.argv[1])

    if file.isValid() : 
        searchInformation(file)
        return 0

    print("Failure")
    return -1


def searchInformation(resfile) :
    """
    Display parameters from the ms_mascotresfile 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.
    """

    fmt = "%-20s: %s"

    print("Search information from ms_mascotresfile")
    print("========================================")
    print(fmt % ("Number of queries"   , resfile.getNumQueries()))
    print(fmt % ("Number of hits"      , resfile.getNumHits()))
    print(fmt % ("Number of sequences" , resfile.getNumSeqs()))
    print(fmt % ("Sequences after tax" , resfile.getNumSeqsAfterTax()))
    print(fmt % ("Number of residues"  , resfile.getNumResidues()))
    print(fmt % ("Execution time"      , resfile.getExecTime()))
    print(fmt % ("Date (seconds)"      , resfile.getDate()))

    date = time.localtime(resfile.getDate())
    Wdays = "Mon Tue Wed Thu Fri Sat Sun".split(" ")
    Mons = "Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec".split(" ")

    print(fmt %( "Date", "%s %s %d %02d:%02d:%02d %d" % (
        Wdays[date.tm_wday],
        Mons[date.tm_mon - 1],
        date.tm_mday,
        date.tm_hour,
        date.tm_min,
        date.tm_sec,
        date.tm_year
        )))

    print(fmt % ("Mascot version"       , resfile.getMascotVer()))
    print(fmt % ("Fasta version"        , resfile.getFastaVer()))
    print(fmt % ("Is PMF?"              , resfile.isPMF()))
    print(fmt % ("Is MSMS?"             , resfile.isMSMS()))
    print(fmt % ("Is SQ?"               , resfile.isSQ()))
    print(fmt % ("Is Error tolerant"    , resfile.isErrorTolerant()))
    print(fmt % ("Any PMF?"             , resfile.anyPMF()))
    print(fmt % ("Any MSMS?"            , resfile.anyMSMS()))
    print(fmt % ("Any SQ?"              , resfile.anySQ()))
    print(fmt % ("Any peptides section" , resfile.doesSectionExist(msparser.ms_mascotresfile.SEC_PEPTIDES)))
    print(fmt % ("Any peptide matches"  , resfile.anyPeptideSummaryMatches()))

    print(" ")


if __name__ == "__main__":
    sys.exit(main())


""" Running the program as

python resfile_info.py F981123.dat

will give the following output under Mascot Server 2.3:

Search information from ms_mascotresfile
========================================
Number of queries   : 67
Number of hits      : 50
Number of sequences : 257964
Sequences after tax : 257964
Number of residues  : 93947433.0
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?             : False
Is MSMS?            : True
Is SQ?              : False
Is Error tolerant   : False
Any PMF?            : False
Any MSMS?           : True
Any SQ?             : False
Any peptides section: True
Any peptide matches : True


"""

Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:50