config_modfile.py

Read in the modifications file - modfile.

#!/usr/bin/python
 
 
import msparser
import sys
 
if len(sys.argv) < 3:
    print("Usage: %s UNIMOD  SCHEMA" % sys.argv[0])
    print("UNIMOD is the file path to the unimod.xml file, e.g., ../config/unimod.xml or a fully formed URL such as http://www.matrixscience.com/cgi .")
    print("SCHEMA is the unimod schema file path, e.g., ../html/xmlns/schema/unimod_2/unimod_2.xsd")
    sys.exit(1)
 
umodFile = msparser.ms_umod_configfile(sys.argv[1], sys.argv[2])
file = msparser.ms_modfile(umodFile)
 
if not file.isValid() :
    print("There are errors. Cannot continue. The last error description:")
    print(file.getLastErrorString())
    sys.exit(1)
 
n = file.getNumberOfModifications()
print("There are %d modifications configured:" % n)
 
for i in range(n) :
    print(file.getModificationByNumber(i).getTitle())
 
 
# Now change Acetyl (K).
mod = file.getModificationByName("Acetyl (K)")
mod.setHidden(True)
file.updateModificationByName("Acetyl (K)", mod)
 
# And delete Methyl (R).
file.deleteModificationByName("Methyl (R)")
 
# Finally, save the file under a new name.
file.setFileName(sys.argv[1] + ".new")
file.save_file()
 
if not file.isValid() :
    print("Failed to save: %s" % file.getLastErrorString())
else :
    print("%s.new now has %d modifications configured" % (sys.argv[1], file.getNumberOfModifications()))
 
 
 
"""
 
Running the program as 
 
python config_modfile.py ../config/unimod.xml ../html/xmlns/schema/unimod_2/unimod_2.xsd
 
will give the following output under Mascot Server 2.3:
 
 
There are 886 modifications configured:
15dB-biotin (C)
2-succinyl (C)
2HPG (R)
3-deoxyglucosone (R)
3sulfo (N-term)
4-ONE (C)
4-ONE (H)
4-ONE (K)
4-ONE+Delta:H(-2)O(-1) (C)
4-ONE+Delta:H(-2)O(-1) (H)
4-ONE+Delta:H(-2)O(-1) (K)
4AcAllylGal (C)
a-type-ion (C-term)
AccQTag (K)
AccQTag (N-term)
Acetyl (C)
    [...]
Xlink:B10621 (C)
Xlink:DMP (K)
Xlink:DMP (Protein N-term)
Xlink:DMP-s (K)
Xlink:DMP-s (Protein N-term)
Xlink:novobiocin (N-term)
Xlink:SSD (K)
ZGB (K)
ZGB (N-term)
/usr/local/mascot/config/mod_file.new now has 885 modifications configured
 
 
"""