Mercurial > repos > jay > pdaug_basic_plots
diff PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.py @ 5:4c3242563796 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
author | jay |
---|---|
date | Thu, 28 Jan 2021 03:46:16 +0000 |
parents | 7d247e27ff11 |
children |
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--- a/PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.py Tue Jan 12 18:47:41 2021 +0000 +++ b/PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.py Thu Jan 28 03:46:16 2021 +0000 @@ -43,10 +43,10 @@ return df -def Decriptor_generator(InFile, Lamda, Weight, DesType, Out_file): +def Decriptor_generator(infile, lamda, weight, maxlag, destype, out_file): list_pep_name = [] - f = open(InFile) + f = open(infile) lines = f.readlines() for line in lines: @@ -62,62 +62,71 @@ protein = PyPro() protein.ReadProteinSequence(seq) - if DesType == 'PAAC': - DS = protein.GetPAAC(lamda=int(Lamda), weight=float(Weight)) + + if destype == "GetAAComp": + DS = protein.GetAAComp() df = pd.DataFrame(DS, index=[0]) - elif DesType == 'APAAC': - DS = protein.GetAPAAC(lamda=int(Lamda), weight=float(Weight)) - df = pd.DataFrame(DS, index=[0]) - elif DesType == 'CTD': - DS = protein.GetCTD() - df = pd.DataFrame(DS, index=[0]) - elif DesType == 'DPComp': + elif destype == "GetDPComp": DS = protein.GetDPComp() df = pd.DataFrame(DS, index=[0]) - elif DesType == 'GearyAuto': - DS = protein.GetGearyAuto() + elif destype == "GetTPComp": + DS = protein.GetTPComp() df = pd.DataFrame(DS, index=[0]) - elif DesType == 'MoranAuto': - DS = protein.GetMoranAuto() - df = pd.DataFrame(DS, index=[0]) - elif DesType == 'MoreauBrotoAuto': + elif destype == "GetMoreauBrotoAuto": DS = protein.GetMoreauBrotoAuto() df = pd.DataFrame(DS, index=[0]) - elif DesType == 'QSO': - DS = protein.GetQSO() + elif destype =="GetMoranAuto": + DS = protein.GetMoranAuto() + df = pd.DataFrame(DS, index=[0]) + elif destype =="GetGearyAuto": + DS = protein.GetGearyAuto() + df = pd.DataFrame(DS, index=[0]) + elif destype == "GetCTD": + DS = protein.GetCTD() df = pd.DataFrame(DS, index=[0]) - elif DesType == 'SOCN': - DS = protein.GetSOCN() + elif destype == "GetPAAC": + DS = protein.GetPAAC(lamda=int(lamda), weight=float(weight)) df = pd.DataFrame(DS, index=[0]) - elif DesType == 'TPComp': - DS = protein.GetTPComp() + elif destype == "GetAPAAC": + DS = protein.GetAPAAC(lamda=int(lamda), weight=float(weight)) + df = pd.DataFrame(DS, index=[0]) + elif destype =="GetSOCN": + DS = protein.GetSOCN(maxlag=int(maxlag)) df = pd.DataFrame(DS, index=[0]) - elif DesType == 'All': - DS_1 = protein.GetPAAC(lamda=int(Lamda), weight=float(Weight)) - DS_2 = protein.GetAPAAC(lamda=int(Lamda), weight=float(Weight)) - DS_3 = protein.GetCTD() - DS_4 = protein.GetDPComp() - DS_5 = protein.GetGearyAuto() - DS_6 = protein.GetMoranAuto() - DS_7 = protein.GetMoreauBrotoAuto() - DS_8 = protein.GetQSO() - DS_9 = protein.GetSOCN() - DS_10 = protein.GetTPComp() + elif destype =="GetQSO": + DS = protein.GetQSO(maxlag=int(maxlag), weight=float(weight)) + df = pd.DataFrame(DS, index=[0]) + elif destype == "GetTriad": + DS = protein.GetTriad() + df = pd.DataFrame(DS, index=[0]) + elif destype == "All": + DS1 = protein.GetAAComp() + DS2 = protein.GetDPComp() + DS3 = protein.GetTPComp() + DS4 = protein.GetMoreauBrotoAuto() + DS5 = protein.GetMoranAuto() + DS6 = protein.GetGearyAuto() + DS7 = protein.GetCTD() + DS8 = protein.GetPAAC(lamda=int(lamda), weight=float(weight)) + DS9 = protein.GetAPAAC(lamda=int(lamda), weight=float(weight)) + DS10 = protein.GetSOCN(maxlag=int(maxlag)) + DS11 = protein.GetQSO(maxlag=int(maxlag), weight=float(weight)) + DS12 = protein.GetTriad() DS = {} - for D in (DS_1, DS_2, DS_3, DS_4, DS_5, DS_6, DS_7, DS_8, DS_9, DS_10): + for D in (DS1,DS2,DS3,DS4,DS5,DS6,DS7,DS8,DS9,DS10,DS11,DS12): + print(D) DS.update(D) - df = pd.DataFrame(DS, index=[0]) - if DesType == 'BinaryDescriptor': + if destype == 'BinaryDescriptor': out_df = BinaryDescriptor(list_pep_name) else: out_df = pd.concat([out_df, df], axis=0) - out_df.to_csv(Out_file, index=False, sep='\t') + out_df.to_csv(out_file, index=False, sep='\t') if __name__=="__main__": @@ -141,7 +150,12 @@ required=False, default=0.5, help="pep file") - + + parser.add_argument("-m", "--MaxLag", + required=False, + default=10, + help="pep file") + parser.add_argument("-t", "--DesType", required=True, default=None, @@ -153,6 +167,6 @@ help="Path to target tsv file") args = parser.parse_args() - Decriptor_generator(args.InFile, args.Lamda, args.Weight, args.DesType, args.Out_file) + Decriptor_generator(args.InFile, args.Lamda, args.Weight, args.MaxLag, args.DesType, args.Out_file) \ No newline at end of file