1 /** @source ontogetdown
2 **
3 ** Find ontology terms by parent 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 ontogetdown **********************************************************
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 AjPOboall oboall = NULL;
79 AjPOutfile outfile = NULL;
80 AjBool obsolete = ajFalse;
81
82 AjPObo obo = NULL;
83 AjPObo obochild = NULL;
84 AjPOboin obochildin = NULL;
85 AjPStr obochildqry = NULL;
86 AjPTable obotable = NULL;
87
88 ajuint ifound = 0;
89 ajuint ichild = 0;
90 ajuint ikeep = 0;
91
92 AjPList obolist = NULL;
93
94 /* ACD processing */
95 embInit("ontogetdown", argc, argv);
96
97 oboall = ajAcdGetOboall("oboterms");
98 outfile = ajAcdGetOutobo("outfile");
99 obsolete = ajAcdGetBoolean("obsolete");
100
101 /* Application logic */
102 /* Check EDAM ontology (edam.obo) is installed indexed.
103 Loop through queryable fields
104 :Return list of EDAM ids with fields matching keyword(s)
105 Merge lists of matching entries
106 Write output file */
107
108 obochildin = ajOboinNew();
109
110 obochild = ajOboNew();
111
112 obolist = ajListNew();
113
114 obotable = ajTablestrNew(600);
115
116 while(ajOboallNext(oboall, &obo))
117 {
118 if(!obsolete && ajOboIsObsolete(obo))
119 continue;
120
121 ifound++;
122
123 ajFmtPrintS(&obochildqry, "%S-isa:%S", ajOboGetDb(obo), obo->Id);
124 ajOboinQryS(obochildin, obochildqry);
125 while(ajOboinRead(obochildin, obochild))
126 {
127 ichild++;
128 if(!ajTableMatchS(obotable, obochild->Id))
129 {
130 ajObooutWrite(outfile, obochild);
131 ajTablePut(obotable, ajStrNewS(obochild->Id),
132 (void *) 1);
133 ikeep++;
134 }
135 }
136 }
137
138 if(!ifound)
139 ajErr("No matching terms");
140 else if(!ichild)
141 ajErr("No child terms");
142
143 /* Memory clean-up and exit */
144
145 ajStrDel(&obochildqry);
146 ajTablestrFreeKey(&obotable);
147
148 ajOboallDel(&oboall);
149 ajOboinDel(&obochildin);
150
151 ajOboDel(&obo);
152 ajOboDel(&obochild);
153
154 ajListFree(&obolist);
155
156 ajOutfileClose(&outfile);
157
158 embExit();
159
160 return 0;
161 }
162
163
164 /* ==================================================================== */
165 /* ============================ functions ============================= */
166 /* ==================================================================== */
167
168