Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/srptGameXmlMaker.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 #!/usr/bin/env python
2
3 import user, os, sys, getopt, ConfigParser
4 from os import listdir
5
6 def setup_env():
7 if "REPET_PATH" in os.environ.keys():
8 sys.path.append( os.environ["REPET_PATH"] )
9 else:
10 print "*** Error: no environment variable REPET_PATH ***"
11 sys.exit(1)
12 setup_env()
13
14 from pyRepet.sql.RepetDBMySQL import *
15 from pyRepet.gamexml.Xml_writer import *
16 from pyRepet.gamexml.computational import *
17
18 #------------------------------------------------------------------------------
19
20 def help():
21
22 print ""
23 print "usage:",sys.argv[0],"[options]"
24 print "options:"
25 print " -h: this help"
26 print " -f: fasta file (required to generate new '.gamexml' files)"
27 print " -n: annotation tier_name"
28 print " -g: gamexml file (for Apollo). If it's not mentionned, all '.gamexml' files will be updated with the result file"
29 print " -l: light gameXML file (without sequence)"
30 print " -r: result files (require -n)"
31 print " -R: reverse the query and subject of Blaster results"
32 print " -s: tier_name of an annotation to remove from a gameXML file"
33 print " -t: file of table name to use to create the gamexml files (tier name 'tab' format 'tab' table name)"
34 print " -c: configuration file from TEdenovo or TEannot pipeline"
35 print " -H: MySQL host (if no configuration file)"
36 print " -U: MySQL user (if no configuration file)"
37 print " -P: MySQL password (if no configuration file)"
38 print " -D: MySQL database (if no configuration file)"
39 print " -v: verbose (default=0/1/2)"
40 print ""
41
42 #------------------------------------------------------------------------------
43
44 def automatisation( result_file, tier_name, reverse, comput ):
45
46 if verbose > 1:
47 print "Auto update"; sys.stdout.flush()
48 writer = Xml_writer()
49 file_liste = []
50 liste_comp = []
51 liste_comp = listdir('./')
52
53 if result_file != "":
54 for j in liste_comp:
55 if writer.file_in_keys( j, comput ):
56 file_liste = file_liste + [j]
57
58 for i in file_liste:
59 writer.update_gamexml( i, result_file, tier_name, comput )
60
61 else:
62 for j in liste_comp:
63 if j.find( "gamexml" ) != -1:
64 writer.parse_gamexml( j )
65 writer.verif_name_prog( tier_name )
66 writer.write( j )
67 if verbose > 1:
68 print tier_name + " program from " +j +" removed"
69
70 #------------------------------------------------------------------------------
71
72 def main():
73
74 f_result = ""
75 f_gamexml = ""
76 f_fasta = ""
77 f_table = ""
78 tier_name = ""
79 substract_name = ""
80 no_seq = 0
81 configFileName = ""
82 host = ""
83 user = ""
84 passwd = ""
85 dbname = ""
86 verbose = 0
87
88 try:
89 options,arguments=getopt.getopt(sys.argv[1:],"hn:f:g:r:s:lRt:c:H:U:P:D:v:",["help","tier_name=","fasta","gamexml","result","substract_program","light","reverse_result","table"])
90 except getopt.GetoptError:
91 help()
92 sys.exit(1)
93 if options == []:
94 help()
95 sys.exit(1)
96 for o,a in options:
97 if o == "-h" or o == "--help":
98 help()
99 sys.exit(0)
100 elif o == "-f" or o == "--fasta":
101 f_fasta = a
102 elif o == "-g" or o == "--gamexml":
103 f_gamexml = a
104 elif o == "-n" or o == "--tier_name":
105 tier_name = a
106 elif o == "-r" or o == "--result":
107 f_result = a
108 elif o == "-s" or o == "--subtract_program":
109 substract_name = a
110 elif o == "-l" or o == "--light":
111 no_seq = 1
112 elif o == "-R" or o == "--reverse_result":
113 writer.set_reverse()
114 elif o == "-t" or o == "--table":
115 f_table = a
116 elif o == "-c":
117 configFileName = a
118 elif o == "-H":
119 host = a
120 elif o == "-U":
121 user = a
122 elif o == "-P":
123 passwd = a
124 elif o == "-D":
125 dbname = a
126 elif o == "-v":
127 verbose = int(a)
128
129 if tier_name == "" and substract_name == "" and f_result != "":
130 print "*** Error: option -n required"
131 help()
132 sys.exit(1)
133
134 if f_fasta == "" and f_gamexml == "":
135 print "*** Error: options -g or -f required"
136 help()
137 sys.exit(1)
138
139 if substract_name!="" and f_result!="" :
140 print "Error: option -s and -r together"
141 help()
142 sys.exit(1)
143
144
145 if verbose > 0:
146 print "\nbeginning of %s" % (sys.argv[0].split("/")[-1])
147 sys.stdout.flush()
148
149 if configFileName != "":
150 config = ConfigParser.ConfigParser()
151 config.readfp( open(configFileName) )
152 host = config.get("repet_env","repet_host")
153 user = config.get("repet_env","repet_user")
154 passwd = config.get("repet_env","repet_pw")
155 dbname = config.get("repet_env","repet_db")
156
157 if host == "" and os.environ.get( "REPET_HOST" ) != None:
158 host = os.environ.get( "REPET_HOST" )
159 if user == "" and os.environ.get( "REPET_USER" ) != None:
160 user = os.environ.get( "REPET_USER" )
161 if passwd == "" and os.environ.get( "REPET_PW" ) != None:
162 passwd = os.environ.get( "REPET_PW" )
163 if dbname == "" and os.environ.get( "REPET_DB" ) != None:
164 dbname = os.environ.get( "REPET_DB" )
165
166 writer = Xml_writer()
167
168 # create the dico
169 comput = computational()
170
171 # create all the ".gamexml" files (option '-f')
172 if f_fasta != "":
173 writer.create_gamexml( f_fasta, f_result, tier_name, comput, no_seq )
174
175 #
176 if f_result != "":
177 if f_gamexml != "":
178 key = ".".join( f_gamexml.split(".")[:-1] )
179 else:
180 key = ""
181 format = writer.find_type_file( f_result )
182 resFile = open( f_result )
183 if format == "path":
184 comput.load_dico_path_from_file( key, f_result )
185
186 if f_table != "":
187 if verbose > 1:
188 print "parsing file %s... " % ( f_gamexml ); sys.stdout.flush()
189 writer.parse_gamexml( f_gamexml )
190
191 if f_gamexml != "":
192 ## key=".".join(f_gamexml.split(".")[:-1])
193 key = f_gamexml.split(".")[0]
194 else:
195 key = ""
196
197 tfile = open( f_table )
198 lines = tfile.readlines()
199 for l in lines:
200 if l[0] == "#":
201 continue
202 tok = l.split()
203 #print tok
204 if len(tok) == 0:
205 break
206 tier_name = tok[0]
207 format = tok[1]
208 table = tok[2]
209 alias = ""
210 if verbose > 1:
211 print "table: " + table + " (format=" + format + ")"
212 if len(tok) > 3:
213 alias = tok[3]
214 if verbose > 1:
215 print " alias=" + alias
216
217 if host == "" or user == "" or passwd == "" or dbname == "":
218 print "*** Error: missing information about MySQL connection"
219 sys.exit(1)
220 db = RepetDB( user, host, passwd, dbname )
221
222 if format == "path":
223 comput.load_dico_path_from_table( db, key, table, alias )
224 writer.update_gamexml_comput( tier_name, comput )
225 elif format == "rpath":
226 comput.load_dico_rpath_from_table( db, key, table, alias )
227 elif format == "ipath":
228 comput.load_dico_ipath_from_table( db, key, table, alias )
229 writer.update_gamexml_comput( tier_name, comput )
230 elif format == "align":
231 comput.load_dico_align_from_table( db, key, table, alias )
232 writer.update_gamexml_comput( tier_name, comput )
233 elif format == "map":
234 comput.load_dico_map_from_table( db, key, table, alias )
235 writer.update_gamexml_comput( tier_name, comput )
236 elif format == "rmap":
237 comput.load_dico_rmap_from_table( db, key, table, alias )
238 writer.update_gamexml_comput( tier_name, comput )
239 elif format == "set":
240 comput.load_dico_set_from_table( db, key, table, alias )
241 writer.update_gamexml_comput( tier_name, comput )
242 elif format == "annot":
243 comput.load_dico_annot_from_table( db, key, table, alias )
244 writer.update_gamexml_annot( table, comput )
245 elif format == "annot_set":
246 comput.load_dico_annotset_from_table( db, key, table, alias )
247 writer.update_gamexml_annot( table, comput )
248 else:
249 print "*** Error: unknown format '%s'" % ( format )
250 sys.exit(1)
251 writer.write(f_gamexml)
252
253 db.close()
254
255 #
256 if f_gamexml == "" and f_result != "" and f_fasta == "":
257 automatisation( f_result, tier_name, writer.get_reverse(), comput )
258
259 # update a ".gamexml" file (options '-g' and '-t')
260 if f_gamexml != "" and f_result != "":
261 writer.update_gamexml( f_gamexml, f_result, tier_name, comput )
262
263 # remove a comput
264 if substract_name != "" and tier_name == "":
265 if f_gamexml != "":
266 writer.parse_gamexml( f_gamexml )
267 writer.verif_name_prog( substract_name )
268 writer.write( f_gamexml )
269 if verbose > 1:
270 print substract_name + " program from " + f_gamexml +" removed"
271 else:
272 automatisation( "", substract_name, 0, None )
273
274 if verbose > 0:
275 print "%s finished successfully\n" % (sys.argv[0].split("/")[-1])
276 sys.stdout.flush()
277
278 return 0
279
280 #------------------------------------------------------------------------------
281
282 if __name__ == '__main__':
283 main()