resfile_info.py

Example program for retrieving general search information.

#!/usr/bin/python
 
 
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_mascotresfilebase.createResfile(sys.argv[1])
 
    if file.isValid() : 
        searchInformation(file)
        return 0
 
    print("Failure")
    return -1
 
 
def searchInformation(resfile) :
    """
    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.
    """
 
    fmt = "%-20s: %s"
 
    print("Search information from ms_mascotresfilebase")
    print("========================================")
    print(fmt % ("Number of queries"   , resfile.getNumQueries()))
    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 peptide matches"  , resfile.anyFastaMatches()))
 
    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_mascotresfilebase
========================================
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 peptide matches : True
 
 
"""