Mercurial > repos > jay > pdaug_word_vector_descriptor
diff PDAUG_Peptide_Global_Descriptors/PDAUG_Peptide_Global_Descriptors.py @ 0:a3a1d9bea1ad draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 02:29:04 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Global_Descriptors/PDAUG_Peptide_Global_Descriptors.py Wed Oct 28 02:29:04 2020 +0000 @@ -0,0 +1,117 @@ +from modlamp.descriptors import * +import os +import pandas as pd + +def Descriptor_calcultor(DesType, inputfile, ph, amide,OutFile ): + + list_pep_name = [] + f = open(inputfile) + lines = f.readlines() + + for line in lines: + if ">" in line: + pass + else: + list_pep_name.append(line.strip('\n')) + + desc = GlobalDescriptor(list_pep_name) + + if DesType == "Length": + desc.length() + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "Weight": + + desc.calculate_MW() + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "Charge": + desc.calculate_charge(ph=int(ph), amide=amide) + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "ChargeDensity": + desc.charge_density(ph=int(ph), amide=amide) + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "IsoelectricPoint": + desc.isoelectric_point(amide=amide) + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "InstabilityIndex": + desc.instability_index() + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "Aromaticity": + desc.aromaticity() + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "AliphaticIndex": + desc.aliphatic_index() + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "BomanIndex": + desc.boman_index() + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "HydrophobicRatio": + desc.hydrophobic_ratio() + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "All": + desc.calculate_all(ph=int(ph), amide=amide) + df = desc.descriptor + dfN = desc.featurenames + else: + pass + + df = desc.descriptor + dfN = desc.featurenames + dfOut = pd.DataFrame(df,columns=dfN) + + dfOut.to_csv(OutFile, index=False, sep='\t') + +if __name__=="__main__": + + import argparse + + parser = argparse.ArgumentParser() + + parser.add_argument("-t", "--DesType", + required=True, + default=None, + help="Descriptors Type") + + parser.add_argument("-i", "--InFile", + required=True, + default=None, + help="Peptide File") + + parser.add_argument("-p", "--Ph", + required=False, + default=7.0, + help="Ph 0-14") + + parser.add_argument("-a", "--Amide", + required=False, + default="True", + help="True or False") + + parser.add_argument("-O", "--OutFile", + required=False, + default="out.tsv", + help="True or False") + + + args = parser.parse_args() + + Descriptor_calcultor(args.DesType, args.InFile, args.Ph, args.Amide, args.OutFile)