1 /* @source dreg application
2 **
3 ** DNA regular expressions (perl style)
4 **
5 ** @author Copyright (C) Peter Rice
6 ** @@
7 **
8 ** This program is free software; you can redistribute it and/or
9 ** modify it under the terms of the GNU General Public License
10 ** as published by the Free Software Foundation; either version 2
11 ** of the License, or (at your option) any later version.
12 **
13 ** This program is distributed in the hope that it will be useful,
14 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
15 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16 ** GNU General Public License for more details.
17 **
18 ** You should have received a copy of the GNU General Public License
19 ** along with this program; if not, write to the Free Software
20 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
21 ******************************************************************************/
22
23 #include "emboss.h"
24
25
26
27
28 /* @prog dreg *****************************************************************
29 **
30 ** regular expression search of a nucleotide sequence
31 **
32 ******************************************************************************/
33
main(int argc,char ** argv)34 int main(int argc, char **argv)
35 {
36
37 AjPSeqall seqall;
38 AjPRegexp patexp = NULL;
39 AjPPatlistRegex plist = NULL;
40 AjPReport report=NULL;
41 AjPFeattable feat=NULL;
42 AjPSeq seq = NULL;
43 AjPStr str = NULL;
44 AjPStr tmpstr = NULL;
45 AjPStr substr = NULL;
46 ajint adj;
47
48 embInit("dreg", argc, argv);
49
50 report = ajAcdGetReport ("outfile");
51 seqall = ajAcdGetSeqall("sequence");
52 plist = ajAcdGetRegexp("pattern");
53
54 ajFmtPrintAppS (&tmpstr, "Pattern: %S\n", ajAcdGetValue("pattern"));
55 ajReportSetHeaderS(report, tmpstr);
56
57 while(ajSeqallNext(seqall, &seq))
58 {
59 if(ajSeqIsReversed(seq))
60 adj = ajSeqGetLen(seq) - ajSeqGetOffend(seq);
61 else
62 adj = ajSeqGetOffset(seq);
63 ajDebug("begin:%d end:%d len:%d offset:%d offend:%d "
64 "rev:%B nuc:%B adj:%d\n",
65 ajSeqGetBegin(seq), ajSeqGetEnd(seq), ajSeqGetLen(seq),
66 ajSeqGetOffset(seq), ajSeqGetOffend(seq),
67 ajSeqIsReversed(seq), ajSeqIsNuc(seq), adj);
68
69 ajStrAssignS(&str, ajSeqGetSeqS(seq));
70 ajStrFmtUpper(&str);
71 ajDebug("Testing '%s' len: %d %d regex %x\n",
72 ajSeqGetNameC(seq), ajSeqGetLen(seq), ajStrGetLen(str),
73 patexp);
74 feat = ajFeattableNewSeq(seq);
75 embPatlistRegexSearchAll(feat, seq, plist, ajFalse);
76 if(ajFeattableGetSize(feat))
77 (void) ajReportWrite (report,feat,seq);
78
79 ajFeattableDel(&feat);
80 }
81 ajReportSetSeqstats(report, seqall);
82
83 ajReportClose(report);
84 ajReportDel(&report);
85
86 ajSeqallDel(&seqall);
87 ajSeqDel(&seq);
88
89 ajStrDel(&tmpstr);
90 ajStrDel(&substr);
91 ajStrDel(&str);
92 ajPatlistRegexDel(&plist);
93
94 embExit();
95
96 return 0;
97 }
98