Mercurial > repos > xuebing > sharplabtool

comparison tools/data_source/microbial_import_code.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1
2 def load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ):
3 # FIXME: this function is duplicated in the DynamicOptions class. It is used here only to
4 # set data.name in exec_after_process().
5 microbe_info= {}
6 orgs = {}
7
8 filename = "%s/microbial_data.loc" % GALAXY_DATA_INDEX_DIR
9 for i, line in enumerate( open( filename ) ):
10 line = line.rstrip( '\r\n' )
11 if line and not line.startswith( '#' ):
12 fields = line.split( sep )
13 #read each line, if not enough fields, go to next line
14 try:
15 info_type = fields.pop(0)
16 if info_type.upper() == "ORG":
17 #ORG 12521 Clostridium perfringens SM101 bacteria Firmicutes CP000312,CP000313,CP000314,CP000315 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12521
18 org_num = fields.pop(0)
19 name = fields.pop(0)
20 kingdom = fields.pop(0)
21 group = fields.pop(0)
22 chromosomes = fields.pop(0)
23 info_url = fields.pop(0)
24 link_site = fields.pop(0)
25 if org_num not in orgs:
26 orgs[ org_num ] = {}
27 orgs[ org_num ][ 'chrs' ] = {}
28 orgs[ org_num ][ 'name' ] = name
29 orgs[ org_num ][ 'kingdom' ] = kingdom
30 orgs[ org_num ][ 'group' ] = group
31 orgs[ org_num ][ 'chromosomes' ] = chromosomes
32 orgs[ org_num ][ 'info_url' ] = info_url
33 orgs[ org_num ][ 'link_site' ] = link_site
34 elif info_type.upper() == "CHR":
35 #CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1
36 org_num = fields.pop(0)
37 chr_acc = fields.pop(0)
38 name = fields.pop(0)
39 length = fields.pop(0)
40 gi = fields.pop(0)
41 gb = fields.pop(0)
42 info_url = fields.pop(0)
43 chr = {}
44 chr[ 'name' ] = name
45 chr[ 'length' ] = length
46 chr[ 'gi' ] = gi
47 chr[ 'gb' ] = gb
48 chr[ 'info_url' ] = info_url
49 if org_num not in orgs:
50 orgs[ org_num ] = {}
51 orgs[ org_num ][ 'chrs' ] = {}
52 orgs[ org_num ][ 'chrs' ][ chr_acc ] = chr
53 elif info_type.upper() == "DATA":
54 #DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed
55 uid = fields.pop(0)
56 org_num = fields.pop(0)
57 chr_acc = fields.pop(0)
58 feature = fields.pop(0)
59 filetype = fields.pop(0)
60 path = fields.pop(0)
61 data = {}
62 data[ 'filetype' ] = filetype
63 data[ 'path' ] = path
64 data[ 'feature' ] = feature
65
66 if org_num not in orgs:
67 orgs[ org_num ] = {}
68 orgs[ org_num ][ 'chrs' ] = {}
69 if 'data' not in orgs[ org_num ][ 'chrs' ][ chr_acc ]:
70 orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ] = {}
71 orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ][ uid ] = data
72 else: continue
73 except: continue
74 for org_num in orgs:
75 org = orgs[ org_num ]
76 if org[ 'kingdom' ] not in microbe_info:
77 microbe_info[ org[ 'kingdom' ] ] = {}
78 if org_num not in microbe_info[ org[ 'kingdom' ] ]:
79 microbe_info[ org[ 'kingdom' ] ][org_num] = org
80 return microbe_info
81
82 #post processing, set build for data and add additional data to history
83 from galaxy import datatypes, config, jobs, tools
84 from shutil import copyfile
85
86 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
87 base_dataset = out_data.items()[0][1]
88 history = base_dataset.history
89 if history == None:
90 print "unknown history!"
91 return
92 kingdom = param_dict.get( 'kingdom', None )
93 #group = param_dict.get( 'group', None )
94 org = param_dict.get( 'org', None )
95
96 #if not (kingdom or group or org):
97 if not (kingdom or org):
98 print "Parameters are not available."
99 #workflow passes galaxy.tools.parameters.basic.UnvalidatedValue instead of values
100 if isinstance( kingdom, tools.parameters.basic.UnvalidatedValue ):
101 kingdom = kingdom.value
102 if isinstance( org, tools.parameters.basic.UnvalidatedValue ):
103 org = org.value
104
105 GALAXY_DATA_INDEX_DIR = app.config.tool_data_path
106 microbe_info = load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' )
107 new_stdout = ""
108 split_stdout = stdout.split("\n")
109 basic_name = ""
110 for line in split_stdout:
111 fields = line.split("\t")
112 if fields[0] == "#File1":
113 description = fields[1]
114 chr = fields[2]
115 dbkey = fields[3]
116 file_type = fields[4]
117 name, data = out_data.items()[0]
118 data.set_size()
119 basic_name = data.name
120 data.name = data.name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for " + microbe_info[kingdom][org]['name'] + ":" + chr + ")"
121 data.dbkey = dbkey
122 data.info = data.name
123 data = app.datatypes_registry.change_datatype( data, file_type )
124 data.init_meta()
125 data.set_peek()
126 app.model.context.add( data )
127 app.model.context.flush()
128 elif fields[0] == "#NewFile":
129 description = fields[1]
130 chr = fields[2]
131 dbkey = fields[3]
132 filepath = fields[4]
133 file_type = fields[5]
134 newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context ) #This import should become a library
135 newdata.set_size()
136 newdata.extension = file_type
137 newdata.name = basic_name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")"
138 app.model.context.add( newdata )
139 app.model.context.flush()
140 app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset )
141 history.add_dataset( newdata )
142 app.model.context.add( history )
143 app.model.context.flush()
144 try:
145 copyfile(filepath,newdata.file_name)
146 newdata.info = newdata.name
147 newdata.state = jobs.JOB_OK
148 except:
149 newdata.info = "The requested file is missing from the system."
150 newdata.state = jobs.JOB_ERROR
151 newdata.dbkey = dbkey
152 newdata.init_meta()
153 newdata.set_peek()
154 app.model.context.flush()