Mercurial > repos > jay > pdaug_tsvtofasta
view PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.py @ 10:39fc376c99a8 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
author | jay |
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date | Sun, 09 Jan 2022 03:39:01 +0000 |
parents | 95c09c06f655 |
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import pandas as pd from pydpi.pypro import PyPro import os def BinaryDescriptor(seq): BinaryCode = { 'A':"1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", 'C':"0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", 'D':"0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", 'E':"0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", 'F':"0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", 'G':"0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0", 'H':"0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0", 'I':"0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0", 'K':"0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0", 'L':"0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0", 'M':"0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0", 'N':"0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0", 'P':"0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0", 'Q':"0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0", 'R':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0", 'S':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0", 'T':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0", 'V':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0", 'W':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0", 'Y':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1", } lines = [] Df = [] for s in seq: des = [] for n in s: des.append(BinaryCode[n.upper()]) lines.append(','.join(des).split(',')) df = pd.DataFrame(lines) return df def Decriptor_generator(infile, lamda, weight, maxlag, destype, out_file): list_pep_name = [] f = open(infile) lines = f.readlines() for line in lines: if ">" in line: pass else: list_pep_name.append(line.strip('\n')) out_df = pd.DataFrame() for seq in list_pep_name: protein = PyPro() protein.ReadProteinSequence(seq) if destype == "GetAAComp": DS = protein.GetAAComp() df = pd.DataFrame(DS, index=[0]) elif destype == "GetDPComp": DS = protein.GetDPComp() df = pd.DataFrame(DS, index=[0]) elif destype == "GetTPComp": DS = protein.GetTPComp() df = pd.DataFrame(DS, index=[0]) elif destype == "GetMoreauBrotoAuto": DS = protein.GetMoreauBrotoAuto() df = pd.DataFrame(DS, index=[0]) 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 == "GetPAAC": DS = protein.GetPAAC(lamda=int(lamda), weight=float(weight)) df = pd.DataFrame(DS, index=[0]) 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 =="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 (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': 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') if __name__=="__main__": import argparse parser = argparse.ArgumentParser() parser.add_argument("-I", "--InFile", required=True, default=None, help="pep file") parser.add_argument("-l", "--Lamda", required=False, default=50, help="pep file") parser.add_argument("-w", "--Weight", 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, help="out put file name for str Descriptors") parser.add_argument("-O", "--Out_file", required=False, default="Out.tsv", help="Path to target tsv file") args = parser.parse_args() Decriptor_generator(args.InFile, args.Lamda, args.Weight, args.MaxLag, args.DesType, args.Out_file)