config_masses.py

Read in the masses file.

#!/usr/bin/python
##############################################################################
# file: config_masses.pl                                                     #
# This file illustrates how to use ms_masses-class from the Mascot perl      #
# module 'msparser'                                                          #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2010 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#     $Source: parser/examples/test_python/config_masses.py $ #
#     $Author: villek@matrixscience.com $ #
#       $Date: 2018-07-30 16:23:53 +0100 $ #
#   $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $ #
# $NoKeywords::                                                            $ #
##############################################################################

import msparser
import sys

if len(sys.argv) < 2 :
    print("""
The location of masses file has to be specified as a parameter.
The location should either be the full path to the masses file
or a URL to a Mascot server - e.g. http://mascot-server/mascot/cgi
""")
    sys.exit(1)

def checkErrorHandler(obj) :
    print("Last error description                   ")
    print("=========================================")
    print("Error: %s" % obj.getLastErrorString())
    print("=========================================")
    print("Testing the error handling...            ")
    print("=========================================")

    err = obj.getErrorHandler()

    for i in range(1, 1 + err.getNumberOfErrors()) :
        print("Error number: %d (%d times): %s" % (
            err.getErrorNumber(i),
            err.getErrorRepeats(i) + 1,
            err.getErrorString(i)
            ))
    
    print(" ") 

    obj.clearAllErrors()    

# A sessionID can optionally be passed as the second parameter.
# This will only be required if the 'file' is a URL.
if len(sys.argv) > 2 :
    cs = msparser.ms_connection_settings()
    cs.setSessionID(sys.argv[2])
    file = msparser.ms_masses(sys.argv[1], cs)
else :
    file = msparser.ms_masses(sys.argv[1])

# Unlike the other configuration files, it is possible to use ms_masses
# without specifying the filename - in which case it defaults to 
# '../config/masses'.

if not file.isValid() :
    print("Error when reading file: %s" % file.getFileName())
    checkErrorHandler(file)
    sys.exit(1)


print("Name of the file: %s" % file.getFileName())
print("-------------------------------------------------------------")
print("---   Content of masses file                              ---")
print("-------------------------------------------------------------")
print("# Amino acid masses (monoisotopic and average)")

for i in range(0, 26) :
    res = chr(ord('A') + i)
    print("%1s:%5.5f,%5.5f" % (
        res, 
        file.getResidueMass(msparser.MASS_TYPE_MONO, res),
        file.getResidueMass(msparser.MASS_TYPE_AVE, res)
        ))

print (" ")
print("# Atomic masses used for terminus values")

print("HYDROGEN:%5.5f,%5.5f" % (
    file.getHydrogenMass(msparser.MASS_TYPE_MONO),
    file.getHydrogenMass(msparser.MASS_TYPE_AVE)
    ))

print("CARBON:%5.5f,%5.5f" % (
    file.getCarbonMass(msparser.MASS_TYPE_MONO),
    file.getCarbonMass(msparser.MASS_TYPE_AVE)
    ))

print("NITROGEN:%5.5f,%5.5f" % (
    file.getNitrogenMass(msparser.MASS_TYPE_MONO),
    file.getNitrogenMass(msparser.MASS_TYPE_AVE)
    ))

print("OXYGEN:%5.5f,%5.5f" % (
    file.getOxygenMass(msparser.MASS_TYPE_MONO),
    file.getOxygenMass(msparser.MASS_TYPE_AVE)
    ))

print("ELECTRON:%5.7f" % (
    file.getElectronMass()
    ))




"""

Running the program as 

python config_masses.pl /usr/local/mascot/config/masses

will give the following output under Mascot Server 2.3:


Name of the file: /usr/local/mascot/config/masses
-------------------------------------------------------------
---   Content of masses file                              ---
-------------------------------------------------------------
# Amino acid masses (monoisotopic and average)
A:71.03711,71.07790
B:114.53494,114.59500
C:103.00919,103.14290
D:115.02694,115.08740
E:129.04259,129.11400
F:147.06841,147.17390
G:57.02146,57.05130
H:137.05891,137.13930
I:113.08406,113.15760
J:0.00000,0.00000
K:128.09496,128.17230
L:113.08406,113.15760
M:131.04048,131.19610
N:114.04293,114.10260
O:0.00000,0.00000
P:97.05276,97.11520
Q:128.05858,128.12920
R:156.10111,156.18570
S:87.03203,87.07730
T:101.04768,101.10390
U:150.95363,150.03790
V:99.06841,99.13110
W:186.07931,186.20990
X:111.00000,111.00000
Y:163.06333,163.17330
Z:128.55059,128.62160

# Atomic masses used for terminus values
HYDROGEN:1.00783,1.00794
CARBON:12.00000,12.01070
NITROGEN:14.00307,14.00670
OXYGEN:15.99491,15.99940
ELECTRON:0.0005490


"""