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:returns: string containing pParse parameters
.. note:
# pParse.para params template
# For help: mail to tuhuijun@ict.ac.cn
# Time: 2014.12.08
[Basic Options]
datapath = C:\filedirectory\filename
logfilepath = C:\filedirectory
outputpath = C:\filedirectory
[Advanced Options]
co-elute = 1
# 0, output single precursor for single scan;
# 1, output all co-eluted precursors.
input_format = raw
# raw / ms1
isolation_width = 1.6
# 2 / 2.5 / 3 / 4
mars_threshold = -0.5
ipv_file = .\IPV.txt
trainingset = EmptyPath
[Internal Switches]
output_mars_y = 0
delete_msn = 0
output_mgf = 1
output_pf = 1
debug_mode = 0
check_activationcenter = 1
output_all_mars_y = 0
rewrite_files = 0
export_unchecked_mono = 0
cut_similiar_mono = 1
mars_model = 4
output_trainingdata = 0
""""""
output = str()
#Basic options
output = '\n'.join([output, ' = '.join(['datapath', rawfilepath])])
output = '\n'.join([output, ' = '.join(['logfilepath', outputpath])])
output = '\n'.join([output, ' = '.join(['outputpath', outputpath])])
#Advanced options
output = '\n'.join([output, ' = '.join(['co-elute', str(coElute)])])
output = '\n'.join([output, ' = '.join(['input_format', 'raw'])])
output = '\n'.join([output, ' = '.join(['isolation_width',
str(isolationWindow)]
)])
output = '\n'.join([output, ' = '.join(['mars_threshold', '-0.5'])])
output = '\n'.join([output, ' = '.join(['ipv_file', '.\IPV.txt'])])
output = '\n'.join([output, ' = '.join(['trainingset', 'EmptyPath'])])
#Internal Switches
output = '\n'.join([output, ' = '.join(['output_mars_y', '0'])])
output = '\n'.join([output, ' = '.join(['delete_msn', '0'])])
output = '\n'.join([output, ' = '.join(['output_mgf', '1'])])
output = '\n'.join([output, ' = '.join(['output_pf', '0'])])
output = '\n'.join([output, ' = '.join(['debug_mode', '0'])])
output = '\n'.join([output, ' = '.join(['check_activationcenter', '1'])])
output = '\n'.join([output, ' = '.join(['output_all_mars_y', '0'])])
output = '\n'.join([output, ' = '.join(['rewrite_files', '0'])])
output = '\n'.join([output, ' = '.join(['export_unchecked_mono', '0'])])
output = '\n'.join([output, ' = '.join(['cut_similiar_mono', '1'])])
output = '\n'.join([output, ' = '.join(['mars_model', '4'])])
output = '\n'.join([output, ' = '.join(['output_trainingdata', '0'])])
return output"
3757,"def writeParams(rawfilepath, outputpath, isolationWindow, coElute=0):
""""""Generate and write a pParse parameter file.
:param rawfilepath: location of the thermo "".raw"" file
:param outputpath: path to the output directory of pParse
:param isolationWindow: MSn isolation window that was used for the
aquisition of the specified thermo raw file
:param coElute:
:returns: file path of the pParse parameter file
""""""
paramText = generateParams(rawfilepath, outputpath, isolationWindow,
coElute)
filename, fileext = os.path.splitext(os.path.basename(rawfilepath))
paramPath = aux.joinpath(outputpath, filename+'.pparse.para')
with open(paramPath, 'wb') as openfile:
openfile.write(paramText)
return paramPath"
3758,"def execute(paramPath, executable='pParse.exe'):
""""""Execute pParse with the specified parameter file.
:param paramPath: location of the pParse parameter file
:param executable: must specify the complete file path of the pParse.exe
if its location is not in the ``PATH`` environment variable.
:returns: :func:`subprocess.Popen` return code, 0 if pParse was executed
successful
""""""
procArgs = [executable, paramPath]
## run it ##
proc = subprocess.Popen(procArgs, stderr=subprocess.PIPE)