Mercurial > repos > jay > pdaug_peptide_sequence_analysis

comparison PDAUG_Basic_Plots/PDAUG_Basic_Plots.py @ 0:e59674e3a391 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
author jay
date Fri, 20 Nov 2020 19:47:44 +0000
parents
children d11a54691a2f
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equal deleted inserted replaced
-1:000000000000 0:e59674e3a391
1 from wordcloud import WordCloud, STOPWORDS
2 import matplotlib.pyplot as plt
3 import glob, os, sys
4 import pandas as pd
5 import plotly.express as px
6 ###################################
7 from wordcloud import WordCloud, STOPWORDS
8 import matplotlib.pyplot as plt
9
10
11 def ReturnPeptide(Infile):
12
13 file = open(Infile)
14 lines = file.readlines()
15
16 Index = []
17 Pep = []
18
19 for line in lines:
20 if '>' in line:
21 line = line.strip('\n')
22 line = line.strip('\r')
23 Index.append(line.strip('\n'))
24 else:
25 line = line.strip('\n')
26 line = line.strip('\r')
27 Pep.append(line)
28 return Pep, Index
29
30
31 def FragReturn(Seq, d):
32
33 tokens = []
34 for seq in Seq:
35
36 for l in range(d):
37 if l < d:
38 for x in range(int(len(seq)/d)):
39 s = (x*d)+l
40 e = s+d
41 if len(seq[s:e]) == d:
42 tokens.append(seq[s:e])
43
44 else:
45 pass
46 else:
47 pass
48 return tokens
49
50 def PlotWordCloud(TokenList, OutFile):
51
52 comment_words = ''
53 stopwords = set(STOPWORDS)
54 comment_words += " ".join(TokenList)+" "
55
56 wordcloud = WordCloud(width = 800, height = 800,
57 background_color ='white',
58 stopwords = stopwords,
59 min_font_size = 10).generate(comment_words)
60
61 plt.figure(figsize = (8, 8), facecolor = None)
62 plt.imshow(wordcloud)
63 plt.axis("off")
64 plt.tight_layout(pad = 0)
65 plt.savefig(OutFile,dpi=600)
66
67
68 def HeatMapPlot(Infile, IndexColumn, x_label, y_label, Workdirpath, htmlOutDir, htmlFname):
69
70 if not os.path.exists(htmlOutDir):
71 os.makedirs(htmlOutDir)
72
73 df = pd.read_csv(Infile, sep="\t")
74 y_ticks = list(df[IndexColumn])
75
76 fig = px.imshow(df[df.columns.tolist()[1:]], labels=dict(x=x_label, y=y_label), y=y_ticks)
77 fig.update_xaxes(side="top")
78
79 fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname))
80
81
82 def BoxPlot(InFile, Feature, label, Workdirpath, htmlOutDir, htmlFname):
83
84 Workdirpath = os.path.join(os.getcwd(),'report_dir')
85
86 if not os.path.exists(htmlOutDir):
87 os.makedirs(htmlOutDir)
88
89 df = pd.read_csv(InFile, sep="\t")
90 fig = px.box(df, y=Feature, color=label, notched=True, title="Box plot of "+Feature )
91 fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname))
92
93
94 def ScatterPlot(InFile, Feature1, Feature2, Feature3, Label, PlotType, Workdirpath, htmlOutDir, htmlFname):
95
96 Workdirpath = os.path.join(os.getcwd(),'report_dir')
97
98 if not os.path.exists(htmlOutDir):
99 os.makedirs(htmlOutDir)
100
101 df = pd.read_csv(InFile, sep="\t")
102
103
104 if PlotType == "3D":
105 fig = px.scatter_3d(df, x=Feature1, y=Feature2, z=Feature3, color=Label)
106 fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname))
107
108 elif PlotType == "2D":
109 fig = px.scatter(df, x=Feature1, y=Feature2, color=Label)
110 fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname))
111
112
113 def WordCloudPlot(InFile, d, Workdirpath, htmlOutDir, htmlFname):
114
115 Workdirpath = os.path.join(os.getcwd(),'report_dir')
116 if not os.path.exists(htmlOutDir):
117 os.makedirs(htmlOutDir)
118
119 Peps,_ = ReturnPeptide(InFile)
120 Frags = FragReturn(Peps, int(d))
121
122 PlotWordCloud(Frags, "out.png")
123 #HTML_Gen(os.path.join(Workdirpath, htmlOutDir, htmlFname))
124
125
126 if __name__=="__main__":
127
128
129 import argparse
130
131 parser = argparse.ArgumentParser(description='Deployment tool')
132 subparsers = parser.add_subparsers()
133
134 HM = subparsers.add_parser('HeatMap')
135 HM.add_argument("-I", "--InFile", required=True, default=None, help="Path to target tsv file")
136 HM.add_argument("-C", "--IndexColumn", required=True, help="")
137 HM.add_argument("-x", "--x_label", required=True, help="")
138 HM.add_argument("-y","--y_label", required=True, help="")
139 HM.add_argument("--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="Path to html directory")
140 HM.add_argument("--htmlFname", required=False, help="HTML out file", default="report.html")
141 HM.add_argument("--Workdirpath", required=False, default=os.getcwd(), help="Path to working directory")
142
143 BP = subparsers.add_parser('BoxPlot')
144 BP.add_argument("-I", "--InFile", required=True, default=None, help="Input file")
145 BP.add_argument("-F", "--Feature", required=True, default=None, help="Feature list")
146 BP.add_argument("-O", "--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="Path to html dir")
147 BP.add_argument("-Hf", "--htmlFname", required=False, help="HTML out file", default="report.html")
148 BP.add_argument("-Wp", "--Workdirpath", required=False, default=os.getcwd(), help="Path to Working Directory")
149 BP.add_argument("-L", "--Label", required=False, default=False, help="Working Directory Path")
150
151 SP = subparsers.add_parser('ScatterPlot')
152 SP.add_argument("-I", "--InFile", required=True, default=None, help="Path to target tsv file")
153 SP.add_argument("-F1", "--Feature1", required=True, default=True, help="Path to target tsv file")
154 SP.add_argument("-F2", "--Feature2", required=True, default=True, help="Roatate ticks")
155 SP.add_argument("-F3", "--Feature3", required=False, help="Roatate ticks")
156 SP.add_argument("-O","--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir")
157 SP.add_argument("-Hf","--htmlFname", required=False, help="HTML out file", default="jai.html")
158 SP.add_argument("-Wp","--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path")
159 SP.add_argument("-T", "--PlotType", required=True, help="")
160 SP.add_argument("-L","--Label", required=False, default=False, help="Working Directory Path")
161
162 WC = subparsers.add_parser('WordCloud')
163 WC.add_argument("-I", "--InFile", required=True, default=None, help="Path to target tsv file")
164 WC.add_argument("-D", "--FragSize", required=True, default=None, help="Path to target tsv file")
165 WC.add_argument("-O","--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir")
166 WC.add_argument("-Hf","--htmlFname", required=False, help="HTML out file", default="report.html")
167 WC.add_argument("-Wp","--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path")
168
169
170 args = parser.parse_args()
171
172 if sys.argv[1] == "HeatMap":
173 HeatMapPlot(args.InFile, args.IndexColumn, args.x_label, args.y_label, args.Workdirpath, args.htmlOutDir, args.htmlFname)
174
175 elif sys.argv[1] == "ScatterPlot":
176 ScatterPlot(args.InFile, args.Feature1, args.Feature2, args.Feature3, args.Label, args.PlotType, args.Workdirpath, args.htmlOutDir, args.htmlFname)
177
178 elif sys.argv[1] == "BoxPlot":
179 BoxPlot(args.InFile, args.Feature, args.Label, args.Workdirpath, args.htmlOutDir, args.htmlFname)
180
181 elif sys.argv[1] == "WordCloud":
182 WordCloudPlot(args.InFile, args.FragSize, args.Workdirpath, args.htmlOutDir, args.htmlFname)
183
184 else:
185 print("In Correct Option:")