Example program for retrieving search parameter data.
import msparser
import sys
def main() :
if len(sys.argv) < 2 :
print("Must specify results filename as parameter")
return 1
resfile = msparser.ms_mascotresfile(sys.argv[1])
if resfile.isValid() :
searchParameters(resfile)
def searchParameters(resfile) :
"""
Display parameters from the ms_searchparams object.
The values come from the parameters and the masses sections of the file.
"""
params = resfile.params()
fmt = "%-20s: %s"
print("Search parameters from ms_searchparams")
print("=========================================")
print(fmt % ("License" , params.getLICENSE()))
print(fmt % ("Search title" , params.getCOM()))
print(fmt % ("SEG mass" , params.getSEG()))
print(fmt % ("Peptide tol" , params.getTOL()))
print(fmt % ("Peptide tol units" , params.getTOLU()))
print(fmt % ("Fragment tol" , params.getITOL()))
print(fmt % ("Fragment tol units" , params.getITOLU()))
print(fmt % ("Missed cleavages" , params.getPFA()))
print(fmt % ("Database" , params.getDB()))
print(fmt % ("Static mods" , params.getMODS()))
print(fmt % ("Average/monoisotopic", params.getMASS()))
print(fmt % ("Enzyme" , params.getCLE()))
print(fmt % ("Raw data file name" , params.getFILENAME()))
print(fmt % ("Input data" , params.getQUE()))
print(fmt % ("Type of search" , params.getSEARCH()))
print(fmt % ("User name" , params.getUSERNAME()))
print(fmt % ("User email" , params.getUSEREMAIL()))
print(fmt % ("Charge state" , params.getCHARGE()))
print(fmt % ("Repeat search file" , params.getINTERMEDIATE()))
print(fmt % ("Num hits to display" , params.getREPORT()))
print(fmt % ("Show overview" , params.getOVERVIEW()))
print(fmt % ("Data file format" , params.getFORMAT()))
print(fmt % ("Form version" , params.getFORMVER()))
print(fmt % ("Variable mods" , params.getIT_MODS()))
for i in range(12) :
print(fmt % ( "User%02d" % i, params.getUSERField(i)))
print(fmt % ("Precursor mass" , params.getPRECURSOR()))
print(fmt % ("Taxonomy filter" , params.getTAXONOMY()))
print(fmt % ("Type of report" , params.getREPTYPE()))
print(fmt % ("Accessions to search", params.getACCESSION()))
print(fmt % ("Subcluster used" , params.getSUBCLUSTER()))
print(fmt % ("ICAT search?" , params.getICAT()))
print(fmt % ("Instrument type" , params.getINSTRUMENT()))
print(fmt % ("Error tolerant?" , params.getERRORTOLERANT()))
print(fmt % ("Rules (ions series)" , params.getRULES()))
for ch in range(ord('A'), 1 + ord('Z')) :
print(fmt % ("Residue " + chr(ch), params.getResidueMass(chr(ch))))
print(fmt % ("C terminus mass" , params.getCTermMass()))
print(fmt % ("N terminus mass" , params.getNTermMass()))
print(fmt % ("Mass of hydrogen", params.getHydrogenMass()))
print(fmt % ("Mass of oxygen" , params.getOxygenMass()))
print(fmt % ("Mass of carbon" , params.getCarbonMass()))
print(fmt % ("Mass of nitrogen", params.getNitrogenMass()))
print(fmt % ("Mass of electron", params.getElectronMass()))
i = 1
while params.getVarModsName(i) :
print(fmt % ("Variable mod name" , params.getVarModsName(i)))
print(fmt % ("Variable mod delta" , params.getVarModsDelta(i)))
print(fmt % ("Variable mod neutral", params.getVarModsNeutralLoss(i)))
i += 1
print(" ")
if __name__ == "__main__" :
sys.exit(main())
"""
Running the program as
python resfile_params.pl 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 : False
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 :
Precursor mass : 0.0
Taxonomy filter : All entries
Type of report : Peptide
Accessions to search:
Subcluster used : -1
ICAT search? : False
Instrument type : ESI-QUAD-TOF
Error tolerant? : False
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 : 0.0
Residue K : 128.094963
Residue L : 113.084064
Residue M : 131.040485
Residue N : 114.042927
Residue O : 0.0
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 : 111.0
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 : 12.0
Mass of nitrogen : 14.003074
Mass of electron : 0.000549
Variable mod name : Oxidation (M)
Variable mod delta : 15.994919
Variable mod neutral: 0.0
"""
