def main(argv=None):
# try to get arguments and error handling
if argv is None:
argv = sys.argv
# parse options
[config_filename, psm_filename, FT2_filename_list] = parse_options(argv)
wholeDict = parseconfig.parseConfigKeyValues(config_filename)
#sDecoy_Prefix = wholeDict.get("[Protein_Identification]Decoy_Prefix")
sIdentification_HCD = wholeDict.get("[Isobaric_Chemical_Labeling]Identification_Scan{HCD}")
if ("[Isobaric_Chemical_Labeling]Identification_Scan{CID}" in wholeDict) :
sIdentification_CID = wholeDict.get("[Isobaric_Chemical_Labeling]Identification_Scan{CID}")
sIdentification_CID = ""
sMass_Tolerance_Reporter_Ions = wholeDict.get("[Isobaric_Chemical_Labeling]Mass_Tolerance_Reporter_Ions")
sReporter_Ion_Key_dict = parseconfig.getConfigMasterKeyValue ("[Isobaric_Chemical_Labeling]Reporter_Ion", wholeDict)
sIsotopic_Impurity_Correction = wholeDict.get("[Isobaric_Chemical_Labeling]Isotopic_Impurity_Correction")
sReporter_Ion_Isotopic_Impurity_Distribution_Key_dict = {}
if (sIsotopic_Impurity_Correction == "True") :
sReporter_Ion_Isotopic_Impurity_Distribution_Key_dict = parseconfig.getConfigMasterKeyValue ("[Isobaric_Chemical_Labeling]Reporter_Ion_Isotopic_Impurity_Distribution", wholeDict)
# print sReporter_Ion_Isotopic_Impurity_Distribution_Key_dict
sTotal_Intensity_Normalization = wholeDict.get("[Isobaric_Chemical_Labeling]Total_Intensity_Normalization")
sOnly_Use_Unique_Peptides = wholeDict.get("[Isobaric_Chemical_Labeling]Only_Use_Unique_Peptides")
sPeptide_Modification_Symbol = wholeDict.get("[Isobaric_Chemical_Labeling]Peptide_Modification_Symbol")
if (sPeptide_Modification_Symbol == "None") :
sPeptide_Modification_Symbol = ""
[All_FT2Scans_dict, Reporter_Ion_Key_list] = ReadAllFT2Files(FT2_filename_list, sIdentification_HCD, sIdentification_CID, sMass_Tolerance_Reporter_Ions, sReporter_Ion_Key_dict)
Reporter_Ion_list = OrganizeReporterIon(Reporter_Ion_Key_list, sReporter_Ion_Key_dict)
if (sIsotopic_Impurity_Correction == "True") :
IsotopicImpurityCorrect(All_FT2Scans_dict, Reporter_Ion_list, sReporter_Ion_Isotopic_Impurity_Distribution_Key_dict)
HandlePsmFile(psm_filename, All_FT2Scans_dict, Reporter_Ion_list, sTotal_Intensity_Normalization, sPeptide_Modification_Symbol)
def main(argv=None):
# try to get arguments and error handling
if argv is None:
argv = sys.argv
# parse options
[config_filename, psm_filename,
FT2_filename_list] = parse_options(argv)
wholeDict = parseconfig.parseConfigKeyValues(config_filename)
#sDecoy_Prefix = wholeDict.get("[Protein_Identification]Decoy_Prefix")
sIdentification_HCD = wholeDict.get(
"[Isobaric_Chemical_Labeling]Identification_Scan{HCD}")
if ("[Isobaric_Chemical_Labeling]Identification_Scan{CID}" in wholeDict):
sIdentification_CID = wholeDict.get(
"[Isobaric_Chemical_Labeling]Identification_Scan{CID}")
sIdentification_CID = ""
sMass_Tolerance_Reporter_Ions = wholeDict.get(
"[Isobaric_Chemical_Labeling]Mass_Tolerance_Reporter_Ions")
sReporter_Ion_Key_dict = parseconfig.getConfigMasterKeyValue(
"[Isobaric_Chemical_Labeling]Reporter_Ion", wholeDict)
sIsotopic_Impurity_Correction = wholeDict.get(
"[Isobaric_Chemical_Labeling]Isotopic_Impurity_Correction")
sReporter_Ion_Isotopic_Impurity_Distribution_Key_dict = {}
if (sIsotopic_Impurity_Correction == "True"):
sReporter_Ion_Isotopic_Impurity_Distribution_Key_dict = parseconfig.getConfigMasterKeyValue(
"[Isobaric_Chemical_Labeling]Reporter_Ion_Isotopic_Impurity_Distribution",
wholeDict)
# print sReporter_Ion_Isotopic_Impurity_Distribution_Key_dict
sTotal_Intensity_Normalization = wholeDict.get(
"[Isobaric_Chemical_Labeling]Total_Intensity_Normalization")
sOnly_Use_Unique_Peptides = wholeDict.get(
"[Isobaric_Chemical_Labeling]Only_Use_Unique_Peptides")
sPeptide_Modification_Symbol = wholeDict.get(
"[Isobaric_Chemical_Labeling]Peptide_Modification_Symbol")
if (sPeptide_Modification_Symbol == "None"):
sPeptide_Modification_Symbol = ""
[All_FT2Scans_dict, Reporter_Ion_Key_list
] = ReadAllFT2Files(FT2_filename_list, sIdentification_HCD,
sIdentification_CID, sMass_Tolerance_Reporter_Ions,
sReporter_Ion_Key_dict)
Reporter_Ion_list = OrganizeReporterIon(Reporter_Ion_Key_list,
sReporter_Ion_Key_dict)
if (sIsotopic_Impurity_Correction == "True"):
IsotopicImpurityCorrect(
All_FT2Scans_dict, Reporter_Ion_list,
sReporter_Ion_Isotopic_Impurity_Distribution_Key_dict)
HandlePsmFile(psm_filename, All_FT2Scans_dict, Reporter_Ion_list,
sTotal_Intensity_Normalization, sPeptide_Modification_Symbol)
def main(argv=None):
# try to get arguments and error handling
if argv is None:
argv = sys.argv
# parse options
[config_filename, psm_filename, pro2psm_filename] = parse_options(argv)
wholeDict = parseconfig.parseConfigKeyValues(config_filename)
sOnly_Use_Unique_Peptides = wholeDict.get("[Isobaric_Chemical_Labeling]Only_Use_Unique_Peptides")
sReporter_Ion_Key_dict = parseconfig.getConfigMasterKeyValue ("[Isobaric_Chemical_Labeling]Reporter_Ion", wholeDict)
sPeptide_Modification_Symbol = wholeDict.get("[Isobaric_Chemical_Labeling]Peptide_Modification_Symbol")
[ScansInfo_dict, sReporter_Ion_Names_list] = ReadPsmFile(psm_filename, len(sReporter_Ion_Key_dict))
HandlePro2psmFile(pro2psm_filename, ScansInfo_dict, sReporter_Ion_Names_list, sOnly_Use_Unique_Peptides, sPeptide_Modification_Symbol)
def main(argv=None):
# try to get arguments and error handling
if argv is None:
argv = sys.argv
# parse options
[config_filename, psm_filename, pro2psm_filename] = parse_options(argv)
wholeDict = parseconfig.parseConfigKeyValues(config_filename)
sOnly_Use_Unique_Peptides = wholeDict.get(
"[Isobaric_Chemical_Labeling]Only_Use_Unique_Peptides")
sReporter_Ion_Key_dict = parseconfig.getConfigMasterKeyValue(
"[Isobaric_Chemical_Labeling]Reporter_Ion", wholeDict)
sPeptide_Modification_Symbol = wholeDict.get(
"[Isobaric_Chemical_Labeling]Peptide_Modification_Symbol")
[ScansInfo_dict,
sReporter_Ion_Names_list] = ReadPsmFile(psm_filename,
len(sReporter_Ion_Key_dict))
HandlePro2psmFile(pro2psm_filename, ScansInfo_dict,
sReporter_Ion_Names_list, sOnly_Use_Unique_Peptides,
sPeptide_Modification_Symbol)