--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PDAUG_Basic_Plots/PDAUG_Basic_Plots.py	Wed Oct 28 02:10:12 2020 +0000
@@ -0,0 +1,185 @@
+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("In Correct Option:")