Exemplo n.º 1
0
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)
Exemplo n.º 2
0
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)
Exemplo n.º 3
0
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)
Exemplo n.º 4
0
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)