Mercurial > repos > sagun98 > micropita
comparison galaxy_micropita/micropita_prepare.py @ 3:8fb4630ab314 draft default tip
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author | sagun98 |
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date | Thu, 03 Jun 2021 17:07:36 +0000 |
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2:1c5736dc85ab | 3:8fb4630ab314 |
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1 #!/usr/bin/env python | |
2 | |
3 """ | |
4 Author: George Weingart | |
5 Description: Prepare parameters to call micropita | |
6 """ | |
7 | |
8 ##################################################################################### | |
9 #Copyright (C) <2012> | |
10 # | |
11 #Permission is hereby granted, free of charge, to any person obtaining a copy of | |
12 #this software and associated documentation files (the "Software"), to deal in the | |
13 #Software without restriction, including without limitation the rights to use, copy, | |
14 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, | |
15 #and to permit persons to whom the Software is furnished to do so, subject to | |
16 #the following conditions: | |
17 # | |
18 #The above copyright notice and this permission notice shall be included in all copies | |
19 #or substantial portions of the Software. | |
20 # | |
21 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, | |
22 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A | |
23 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT | |
24 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION | |
25 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE | |
26 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. | |
27 ##################################################################################### | |
28 | |
29 __author__ = "George Weingart" | |
30 __copyright__ = "Copyright 2012" | |
31 __credits__ = ["George Weingart"] | |
32 __license__ = "MIT" | |
33 __maintainer__ = "George Weingart" | |
34 __email__ = "george.weingart@gmail.com" | |
35 __status__ = "Development" | |
36 | |
37 import argparse | |
38 from cStringIO import StringIO | |
39 import sys,string,time | |
40 import os | |
41 from time import gmtime, strftime | |
42 from pprint import pprint | |
43 import subprocess | |
44 import blist | |
45 import shlex | |
46 import tempfile | |
47 | |
48 ################################################################################## | |
49 # Modification by George Weingart 5/6/2014 # | |
50 # Using subprocess to invoke the calls to Micropita # | |
51 # and allocating the temporary file using trmpfile # | |
52 ################################################################################## | |
53 | |
54 | |
55 | |
56 | |
57 ################################################################################## | |
58 # Decode Parms # | |
59 ################################################################################## | |
60 def read_params(x): | |
61 parser = argparse.ArgumentParser(description='Micropita Annotate Argparser') | |
62 parser.add_argument('--input', action="store",dest='inputname') | |
63 parser.add_argument('--output', action="store",dest='outputname') | |
64 parser.add_argument('-m', action="store",dest='MParameter') | |
65 parser.add_argument('-n', action="store",dest='NSamples') | |
66 parser.add_argument('--lastmeta', action="store",dest='lastmeta') | |
67 parser.add_argument('--stratify_value', action="store",dest='stratify_value') | |
68 | |
69 | |
70 try: | |
71 parser.add_argument('--feature_method', action="store",dest='feature_method') | |
72 except: | |
73 pass | |
74 try: | |
75 parser.add_argument('--targets', action="store",dest='targets') | |
76 except: | |
77 pass | |
78 try: | |
79 parser.add_argument('--label_value', action="store",dest='label_value') | |
80 except: | |
81 pass | |
82 return parser | |
83 | |
84 | |
85 ################################################################################## | |
86 # Main Program # | |
87 ################################################################################## | |
88 parser = read_params( sys.argv ) | |
89 results = parser.parse_args() | |
90 #root_dir = os.environ.get('micropita_SCRIPT_PATH') | |
91 root_dir = os.path.dirname(os.path.realpath(__file__)) #Find the current directory where the program resides GW 20160810 | |
92 | |
93 | |
94 fname = results.inputname | |
95 input_file = open(fname,'rU') | |
96 input_lines = input_file.readlines() | |
97 input_file.close() | |
98 table_lines = [] | |
99 for x in input_lines: | |
100 first_column = x.split('\t')[0] | |
101 table_lines.append(first_column) | |
102 | |
103 | |
104 | |
105 FileTimeStamp = strftime("%Y%m%d%H%M%S", gmtime()) | |
106 LastMetaInt = 0 | |
107 if results.lastmeta and not results.lastmeta == "None": | |
108 LastMetaInt = int(results.lastmeta) - 1 | |
109 | |
110 StratifyValueInt = 0 | |
111 if results.stratify_value and not results.stratify_value == "None": | |
112 StratifyValueInt = int(results.stratify_value) - 2 | |
113 | |
114 LabelValueInt = 0 | |
115 if results.label_value and not results.label_value == "None": | |
116 LabelValueInt = int(results.label_value) - 1 | |
117 | |
118 stratify_string = "" | |
119 q = '"' | |
120 if not results.stratify_value == '1': | |
121 stratify_string = " --stratify " + q + table_lines[StratifyValueInt] + q + " " | |
122 | |
123 if results.MParameter == "features": | |
124 TBTargets = list() | |
125 TableTargets = results.targets.split(',') | |
126 for t in TableTargets: | |
127 tb_entry = int(t) + LastMetaInt | |
128 TBTargets.append(int(tb_entry)) | |
129 | |
130 | |
131 OutTargetsFile = tempfile.NamedTemporaryFile('w', delete=False ) | |
132 TempTargetsFileName = OutTargetsFile.name | |
133 indx = -1 | |
134 for c in table_lines: | |
135 indx+=1 | |
136 if indx in TBTargets: | |
137 OutputString = table_lines[indx] + "\n" | |
138 OutTargetsFile.write(OutputString) | |
139 OutTargetsFile.close() | |
140 os_command = "python " + \ | |
141 root_dir + \ | |
142 "/MicroPITA.py "+\ | |
143 "--lastmeta " + table_lines[LastMetaInt]+ " " +\ | |
144 "--feature_method " + results.feature_method + " " + \ | |
145 "--target " + TempTargetsFileName + " " +\ | |
146 "-m " + results.MParameter + " " + \ | |
147 "-n " + results.NSamples + " " +\ | |
148 stratify_string + " " +\ | |
149 results.inputname + " " +\ | |
150 results.outputname | |
151 #print os_command | |
152 os.system(os_command) | |
153 argsx = shlex.split(os_command) #Split the command | |
154 try: | |
155 subprocess.check_call(argsx , shell=False) | |
156 except: | |
157 print "The call to micropita failed=============" | |
158 sys.exit(0) | |
159 | |
160 | |
161 | |
162 if results.MParameter == "representative"\ | |
163 or results.MParameter == "diverse"\ | |
164 or results.MParameter == "extreme": | |
165 os_command = "python " + \ | |
166 root_dir + \ | |
167 "/MicroPITA.py "+\ | |
168 "--lastmeta " + table_lines[LastMetaInt]+ " " +\ | |
169 "-m " + results.MParameter + " " + \ | |
170 "-n " + results.NSamples + " " +\ | |
171 stratify_string + " " + \ | |
172 results.inputname + " " +\ | |
173 results.outputname | |
174 argsx = shlex.split(os_command) #Split the command | |
175 try: | |
176 ###os.system(os_command) | |
177 subprocess.check_call(argsx , shell=False) | |
178 except: | |
179 print "The call to micropita failed=============" | |
180 sys.exit(0) | |
181 | |
182 | |
183 | |
184 | |
185 if results.MParameter == "distinct"\ | |
186 or results.MParameter == "discriminant": | |
187 os_command = "python " + \ | |
188 root_dir + \ | |
189 "/MicroPITA.py "+\ | |
190 "--lastmeta " + table_lines[LastMetaInt]+ " " +\ | |
191 "--label " + table_lines[LastMetaInt]+ " " +\ | |
192 "-m " + results.MParameter + " " + \ | |
193 "-n " + results.NSamples + " " +\ | |
194 stratify_string + " " + \ | |
195 results.inputname + " " +\ | |
196 results.outputname | |
197 #print os_command | |
198 argsx = shlex.split(os_command) #Split the command | |
199 try: | |
200 subprocess.check_call(argsx , shell=False) | |
201 except: | |
202 print "The call to micropita failed=============" | |
203 sys.exit(0) |