Mercurial > repos > jay > pdaug_aa_property_based_peptide_generation
view PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.py @ 7:e64307e1733b draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
author | jay |
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date | Sun, 09 Jan 2022 05:06:26 +0000 |
parents | 69a1ba3d6d29 |
children |
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import modlamp from modlamp.datasets import load_AMPvsTM from modlamp.datasets import load_AMPvsUniProt from modlamp.datasets import load_ACPvsTM from modlamp.datasets import load_ACPvsRandom from modlamp.database import query_apd from modlamp.database import query_camp import os import pandas as pd def DataGen(DataBaseType, OutFile, IDs): if DataBaseType == 'AMPvsTMP': data = load_AMPvsTM() elif DataBaseType == 'AMPvsUniProt': data = load_AMPvsUniProt() elif DataBaseType == 'ACPvsTMP': data = load_ACPvsTM() elif DataBaseType == 'ACPvsRandom': data = load_ACPvsRandom() elif DataBaseType == 'query_apd': data = query_apd([int(i) for i in IDs.split(',')]) df = pd.DataFrame(data, columns=['Peptides']) df.to_csv(OutFile, index=False, sep='\t') exit() elif DataBaseType == 'query_camp': data = query_camp([int(i) for i in IDs.split(',')]) df = pd.DataFrame(data, columns=['Peptides']) df.to_csv(OutFile, index=False, sep='\t') exit() else: print ("Enter Correct Values") exit() peptide_data = data.sequences class_label = int(len(peptide_data)/2)*[data.target_names[0]]+int(len(peptide_data)/2)*[data.target_names[1]] peptide_data = pd.DataFrame(peptide_data, columns=['name']) class_label = pd.DataFrame(class_label, columns=['class_label']) df = pd.concat([peptide_data,class_label], axis=1) df.to_csv(OutFile, index=False, sep='\t') if __name__=="__main__": import argparse parser = argparse.ArgumentParser() parser.add_argument("-d", "--DataBaseType", required=True, default=None, help="Name of the dataset ") parser.add_argument("-o", "--OutFile", required=False, default='Out.tsv', help="Out put file name for str descriptors") parser.add_argument("-L", "--List", required=False, default=None, help="List of integer as ID") args = parser.parse_args() DataGen(args.DataBaseType, args.OutFile, args.List)