Mercurial > repos > jay > pdaug_peptide_data_access
view PDAUG_Peptide_Data_Plotting/PDAUG_Peptide_Data_Plotting.py @ 2:c9078a576efe draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 8b18552f6d2b2261efebe1075ff4c18a295b94dd"
author | jay |
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date | Tue, 29 Dec 2020 18:26:34 +0000 |
parents | 6c12ca9f5d88 |
children |
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from modlamp.plot import helical_wheel from modlamp.plot import plot_pde from modlamp.plot import plot_violin from modlamp.plot import plot_aa_distr import pandas as pd import argparse import sys, os parser = argparse.ArgumentParser(description='Deployment tool') subparsers = parser.add_subparsers() HelWhl = subparsers.add_parser('HelWhl') HelWhl.add_argument("-I","--InFile", required=True, default=None, help="Input data file") HelWhl.add_argument("-C","--colorcoding", required=False, default='rainbow', help="available: , charge, polar, simple, amphipathic, none") HelWhl.add_argument("-L","--lineweights", required=False, default=True, help="(boolean) defines whether connection lines decrease in thickness along the sequence") HelWhl.add_argument("-F","--filename", required=False, default="out.png", help="") HelWhl.add_argument("-s","--seq", required=False, default=False, help="") HelWhl.add_argument("-M","--movment", required=False, default=False, help="") HelWhl.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile") PltPde = subparsers.add_parser('PltPde') PltPde.add_argument("-I","--InFile", required=True, default=None, help="Input data file") PltPde.add_argument("-l", "--ClmList", required=True, default=None, help="") PltPde.add_argument("-F","--filename", required=False, default="out.png", help="filename where to safe the plot. default = None > show the plot") PltPde.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile") PltVio = subparsers.add_parser('PltVio') PltVio.add_argument("-I","--InFile", required=True, default=None, help="Input data file") PltVio.add_argument("-l", "--ClmList", required=True, default=None, help="Column list") PltVio.add_argument("-C","--colors", required=False, default=None, help='Data to be plotted') PltVio.add_argument("-B","--bp", required=False, default=False, help="Print a box blot inside violin") PltVio.add_argument("-T","--title", required=False, default=None, help="Title of the plot.") PltVio.add_argument("-a","--axlabels", required=False, default=None, help="list containing the axis labels for the plot") PltVio.add_argument("-M","--y_max", required=False, default=1, help='y-axis maximum.') PltVio.add_argument("-m","--y_min", required=False, default=0, help="y-axis minimum.") PltVio.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile") PltAaDis = subparsers.add_parser('PltAaDis') PltAaDis.add_argument("-I","--InFile", required=True, default=None, help="Input data file") PltAaDis.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile") args = parser.parse_args() if sys.argv[1] == 'HelWhl': f = open(args.InFile) lines = f.readlines() sequence = lines[1].strip('\n') if args.movment == 'true': mvt = True else: mvt = False if args.seq == 'true': sq = True else: sq = False if args.lineweights == 'true': lw = True else: lw = False helical_wheel(sequence, colorcoding=args.colorcoding, lineweights=args.lineweights, filename=args.OutFile, seq=args.seq, moment=mvt) elif sys.argv[1] == 'PltPde': df = pd.read_csv(args.InFile, sep="\t") data = df[args.ClmList.split(',')].as_matrix().T plot_pde(data, filename=args.OutFile) elif sys.argv[1] == 'PltVio': df = pd.read_csv(args.InFile, sep="\t") data = df[args.ClmList.split(',')].as_matrix().T c = ['#0B486B']*len(args.ClmList.split(',')) plot_violin(data, colors=c, bp=True, filename=args.OutFile) elif sys.argv[1] == 'PltAaDis': f = open(args.InFile) lines = f.readlines() sequences = [] for line in lines: if '>' in line: pass else: sequences.append(line.strip('\n')) plot_aa_distr(sequences, color='#0B486B', filename=args.OutFile)