Mercurial > repos > jay > pdaug_basic_plots
view PDAUG_Peptide_Core_Descriptors/PDAUG_Peptide_Core_Descriptors.py @ 0:7d247e27ff11 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 01:52:18 +0000 |
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from modlamp.core import BaseDescriptor from modlamp.descriptors import PeptideDescriptor import pandas as pd import argparse, os parser = argparse.ArgumentParser() parser.add_argument("-I", "--InFile", required=True, default=None, help="Input file") parser.add_argument("-O", "--OutFile", required=True, default=None, help="Output file") parser.add_argument("-N", "--Ngrams", required=True, default=None, help="ngrams") args = parser.parse_args() file = open(args.InFile) lines = file.readlines() Index = [] Pep = [] for line in lines: if '>' in line: Index.append(line.strip('\n')) else: line = line.strip('\n') line = line.strip('\r') Pep.append(line) df = pd.DataFrame() for i, l in enumerate(Pep): D = PeptideDescriptor(l) D.count_ngrams([int(args.Ngrams)]) df1 = pd.DataFrame(D.descriptor, index=["sequence"+str(i),]) df = pd.concat([df, df1], axis=0) df = df.fillna(0) df.to_csv(args.OutFile, sep='\t', index=None)