1 /** @source edamdef
2 **
3 ** Find EDAM ontology terms by identifier
4 **
5 ** @author Copyright (C) 2010 Jon Ison / EMBOSS
6 ** @version 1 First version</replaceable>
7 ** @modified July 2010 Jon Ison First version</replaceable>
8 ** @@
9 **
10 ** This program is free software; you can redistribute it and/or
11 ** modify it under the terms of the GNU General Public License
12 ** as published by the Free Software Foundation; either version 2
13 ** of the License, or (at your option) any later version.
14 **
15 ** This program is distributed in the hope that it will be useful,
16 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
17 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18 ** GNU General Public License for more details.
19 **
20 ** You should have received a copy of the GNU General Public License
21 ** along with this program; if not, write to the Free Software
22 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23 ********************************************************************/
24
25
26 /* ==================================================================== */
27 /* ========================== include files =========================== */
28 /* ==================================================================== */
29
30 #include "emboss.h"
31
32 /* Inclusion of system and local header files goes here */
33
34
35
36 /* ==================================================================== */
37 /* ============================ constants ============================= */
38 /* ==================================================================== */
39
40 /* #define and enum statements go here */
41
42
43
44 /* ==================================================================== */
45 /* ======================== global variables ========================== */
46 /* ==================================================================== */
47
48 /* Global variables definitions go here */
49
50
51
52 /* ==================================================================== */
53 /* ============================== data ================================ */
54 /* ==================================================================== */
55
56 /* Definition of datatypes go here */
57
58
59
60 /* ==================================================================== */
61 /* ==================== function prototypes =========================== */
62 /* ==================================================================== */
63
64 /* Function prototypes for public (external) functions go here */
65
66
67
68
69 /* @prog edamdef **************************************************************
70 **
71 ** Find EDAM ontology 'data' (identifier) terms by keyword
72 **
73 ******************************************************************************/
74
main(int argc,char ** argv)75 int main(int argc, char **argv)
76 {
77 /* Variable declarations */
78 AjPStr query;
79 AjPStr *namespace = NULL;
80 AjPOutfile outfile = NULL;
81 AjBool subclasses = ajTrue;
82 AjBool obsolete = ajFalse;
83
84 AjPObo obo = NULL;
85 AjPObo obotest = NULL;
86 AjPOboin oboin = NULL;
87
88 AjPList obolist = NULL;
89
90 AjPStr oboqry = NULL;
91 AjPStr qrystr = NULL;
92 AjPTable foundtable = NULL;
93 AjPTable nstable = NULL;
94 const AjPStr name = NULL;
95
96 AjPStrTok handle = NULL;
97 ajint i;
98 ajuint ifound = 0;
99 ajuint ikeep = 0;
100
101 /* ACD processing */
102 embInit("edamdef", argc, argv);
103
104 query = ajAcdGetString("query");
105 namespace = ajAcdGetList("namespace");
106 outfile = ajAcdGetOutobo("outfile");
107 subclasses = ajAcdGetBoolean("subclasses");
108 obsolete = ajAcdGetBoolean("obsolete");
109
110 /* Application logic */
111 /* Check EDAM ontology (edam.obo) is installed indexed.
112 Loop through queryable fields
113 :Return list of EDAM ids with fields matching keyword(s)
114 Merge lists of matching entries
115 Write output file */
116
117 oboin = ajOboinNew();
118 obo = ajOboNew();
119
120 obolist = ajListNew();
121
122 foundtable = ajTablestrNew(600);
123 nstable = ajTablestrNew(6);
124
125 for(i=0; namespace[i]; i++)
126 {
127 ajTablePut(nstable, namespace[i], (void*) 1);
128 }
129
130 handle = ajStrTokenNewC(query, ",");
131 while(ajStrTokenNextParse(handle, &qrystr))
132 {
133 ajFmtPrintS(&oboqry, "edam-des:%S", qrystr);
134 ajOboinQryS(oboin, oboqry);
135
136 while(ajOboinRead(oboin, obo))
137 {
138 if(!obsolete && ajOboIsObsolete(obo))
139 continue;
140
141 ajListPushAppend(obolist, ajOboNewObo(obo));
142 if(subclasses)
143 ajOboGetTree(obo, obolist);
144
145 ajDebug("%S '%S' %Lu\n",
146 qrystr, obo->Id, ajListGetLength(obolist));
147 while(ajListGetLength(obolist))
148 {
149 ajListPop(obolist, (void**) &obotest);
150 if(!obsolete && ajOboIsObsolete(obotest))
151 {
152 ajOboDel(&obotest);
153 continue;
154 }
155
156 ifound++;
157 name = ajOboGetNamespace(obotest);
158
159 if(ajTableMatchS(nstable, name))
160 {
161 if(!ajTableMatchS(foundtable, obotest->Id))
162 {
163 ajObooutWrite(outfile, obotest);
164 ajTablePut(foundtable, ajStrNewS(obotest->Id),
165 (void *) 1);
166 ikeep++;
167 }
168 }
169 ajOboDel(&obotest);
170 }
171 }
172 }
173
174 if(!ifound)
175 ajErr("No matching terms");
176 else if(!ikeep)
177 ajErr("No terms in requested namespace");
178
179 /* Memory clean-up and exit */
180
181 ajOboDel(&obo);
182 ajOboinDel(&oboin);
183
184 ajListFree(&obolist);
185
186 ajStrTokenDel(&handle);
187
188 ajStrDel(&query);
189 ajStrDel(&qrystr);
190 ajStrDel(&oboqry);
191
192 ajTablestrFreeKey(&foundtable);
193 ajTableFree(&nstable);
194
195 for(i=0; namespace[i]; i++)
196 ajStrDel(&namespace[i]);
197 AJFREE(namespace);
198
199 ajOutfileClose(&outfile);
200
201 embExit();
202
203 return 0;
204 }
205
206
207 /* ==================================================================== */
208 /* ============================ functions ============================= */
209 /* ==================================================================== */
210
211