Mercurial > repos > jay > pdaug_peptide_structure_builder
view PDAUG_Basic_Plots/PDAUG_Basic_Plots.py @ 7:ab136a857686 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
author | jay |
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date | Sun, 09 Jan 2022 04:30:05 +0000 |
parents | cbeb25386196 |
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from wordcloud import WordCloud, STOPWORDS import matplotlib.pyplot as plt import glob, os, sys import pandas as pd import plotly.express as px ################################### from wordcloud import WordCloud, STOPWORDS import matplotlib.pyplot as plt def ReturnPeptide(Infile): file = open(Infile) lines = file.readlines() Index = [] Pep = [] for line in lines: if '>' in line: line = line.strip('\n') line = line.strip('\r') Index.append(line.strip('\n')) else: line = line.strip('\n') line = line.strip('\r') Pep.append(line) return Pep, Index def FragReturn(Seq, d): tokens = [] for seq in Seq: for l in range(d): if l < d: for x in range(int(len(seq)/d)): s = (x*d)+l e = s+d if len(seq[s:e]) == d: tokens.append(seq[s:e]) else: pass else: pass return tokens def PlotWordCloud(TokenList, OutFile): comment_words = '' stopwords = set(STOPWORDS) comment_words += " ".join(TokenList)+" " wordcloud = WordCloud(width = 800, height = 800, background_color ='white', stopwords = stopwords, min_font_size = 10).generate(comment_words) plt.figure(figsize = (8, 8), facecolor = None) plt.imshow(wordcloud) plt.axis("off") plt.tight_layout(pad = 0) plt.savefig(OutFile,dpi=600) def HeatMapPlot(Infile, IndexColumn, x_label, y_label, Workdirpath, htmlOutDir, htmlFname): if not os.path.exists(htmlOutDir): os.makedirs(htmlOutDir) df = pd.read_csv(Infile, sep="\t") y_ticks = list(df[IndexColumn]) fig = px.imshow(df[df.columns.tolist()[1:]], labels=dict(x=x_label, y=y_label), y=y_ticks) fig.update_xaxes(side="top") fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname)) def BoxPlot(InFile, Feature, label, Workdirpath, htmlOutDir, htmlFname): Workdirpath = os.path.join(os.getcwd(),'report_dir') if not os.path.exists(htmlOutDir): os.makedirs(htmlOutDir) df = pd.read_csv(InFile, sep="\t") fig = px.box(df, y=Feature, color=label, notched=True, title="Box plot of "+Feature ) fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname)) def ScatterPlot(InFile, Feature1, Feature2, Feature3, Label, PlotType, Workdirpath, htmlOutDir, htmlFname): Workdirpath = os.path.join(os.getcwd(),'report_dir') if not os.path.exists(htmlOutDir): os.makedirs(htmlOutDir) df = pd.read_csv(InFile, sep="\t") if PlotType == "3D": fig = px.scatter_3d(df, x=Feature1, y=Feature2, z=Feature3, color=Label) fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname)) elif PlotType == "2D": fig = px.scatter(df, x=Feature1, y=Feature2, color=Label) fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname)) def WordCloudPlot(InFile, d, Workdirpath, htmlOutDir, htmlFname): Workdirpath = os.path.join(os.getcwd(),'report_dir') if not os.path.exists(htmlOutDir): os.makedirs(htmlOutDir) Peps,_ = ReturnPeptide(InFile) Frags = FragReturn(Peps, int(d)) PlotWordCloud(Frags, "out.png") #HTML_Gen(os.path.join(Workdirpath, htmlOutDir, htmlFname)) if __name__=="__main__": import argparse parser = argparse.ArgumentParser(description='Deployment tool') subparsers = parser.add_subparsers() HM = subparsers.add_parser('HeatMap') HM.add_argument("-I", "--InFile", required=True, default=None, help="Path to target tsv file") HM.add_argument("-C", "--IndexColumn", required=True, help="") HM.add_argument("-x", "--x_label", required=True, help="") HM.add_argument("-y","--y_label", required=True, help="") HM.add_argument("--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="Path to html directory") HM.add_argument("--htmlFname", required=False, help="HTML out file", default="report.html") HM.add_argument("--Workdirpath", required=False, default=os.getcwd(), help="Path to working directory") BP = subparsers.add_parser('BoxPlot') BP.add_argument("-I", "--InFile", required=True, default=None, help="Input file") BP.add_argument("-F", "--Feature", required=True, default=None, help="Feature list") BP.add_argument("-O", "--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="Path to html dir") BP.add_argument("-Hf", "--htmlFname", required=False, help="HTML out file", default="report.html") BP.add_argument("-Wp", "--Workdirpath", required=False, default=os.getcwd(), help="Path to Working Directory") BP.add_argument("-L", "--Label", required=False, default=False, help="Working Directory Path") SP = subparsers.add_parser('ScatterPlot') SP.add_argument("-I", "--InFile", required=True, default=None, help="Path to target tsv file") SP.add_argument("-F1", "--Feature1", required=True, default=True, help="Path to target tsv file") SP.add_argument("-F2", "--Feature2", required=True, default=True, help="Roatate ticks") SP.add_argument("-F3", "--Feature3", required=False, help="Roatate ticks") SP.add_argument("-O","--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir") SP.add_argument("-Hf","--htmlFname", required=False, help="HTML out file", default="jai.html") SP.add_argument("-Wp","--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path") SP.add_argument("-T", "--PlotType", required=True, help="") SP.add_argument("-L","--Label", required=False, default=False, help="Working Directory Path") WC = subparsers.add_parser('WordCloud') WC.add_argument("-I", "--InFile", required=True, default=None, help="Path to target tsv file") WC.add_argument("-D", "--FragSize", required=True, default=None, help="Path to target tsv file") WC.add_argument("-O","--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir") WC.add_argument("-Hf","--htmlFname", required=False, help="HTML out file", default="report.html") WC.add_argument("-Wp","--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path") args = parser.parse_args() if sys.argv[1] == "HeatMap": HeatMapPlot(args.InFile, args.IndexColumn, args.x_label, args.y_label, args.Workdirpath, args.htmlOutDir, args.htmlFname) elif sys.argv[1] == "ScatterPlot": ScatterPlot(args.InFile, args.Feature1, args.Feature2, args.Feature3, args.Label, args.PlotType, args.Workdirpath, args.htmlOutDir, args.htmlFname) elif sys.argv[1] == "BoxPlot": BoxPlot(args.InFile, args.Feature, args.Label, args.Workdirpath, args.htmlOutDir, args.htmlFname) elif sys.argv[1] == "WordCloud": WordCloudPlot(args.InFile, args.FragSize, args.Workdirpath, args.htmlOutDir, args.htmlFname) else: print("Incorrect option provided: %s" % (sys.argv[1]))