1 /* @source fuzznuc application
2 **
3 ** Finds fuzzy patterns in nucleic acid sequences
4 ** @author Copyright (C) Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
5 ** @author modified: Copyright (C) Henrikki Almusa, Medicel Oy
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 fuzznuc **************************************************************
29 **
30 ** Nucleic acid pattern search
31 **
32 ******************************************************************************/
33
main(int argc,char ** argv)34 int main(int argc, char **argv)
35 {
36 AjPSeqall seqall = NULL;
37 AjPSeq seq = NULL;
38 AjPFeattable tab = NULL;
39 AjPReport report = NULL;
40 AjPStr tmpstr = NULL;
41 AjPPatlistSeq plist = NULL;
42 AjBool writeok = ajTrue;
43 AjBool sc;
44
45 embInit("fuzznuc", argc, argv);
46
47 seqall = ajAcdGetSeqall("sequence");
48 report = ajAcdGetReport("outfile");
49 plist = ajAcdGetPattern("pattern");
50 sc = ajAcdGetBoolean("complement");
51
52 ajPatlistSeqDoc(plist, &tmpstr);
53 ajFmtPrintAppS(&tmpstr, "\nComplement: %B\n", sc);
54 ajReportSetHeaderS(report, tmpstr);
55
56 writeok=ajTrue;
57 while (writeok && ajSeqallNext(seqall,&seq))
58 {
59 tab = ajFeattableNewSeq(seq);
60 embPatlistSeqSearchAll(tab,seq,plist,ajFalse);
61 if (sc)
62 embPatlistSeqSearchAll(tab,seq,plist,ajTrue);
63 if(ajFeattableGetSize(tab))
64 writeok = ajReportWrite(report,tab,seq);
65 ajFeattableDel(&tab);
66 }
67
68 ajPatlistSeqDel(&plist);
69
70 ajStrDel(&tmpstr);
71
72 ajReportSetSeqstats(report, seqall);
73 ajReportClose(report);
74 ajReportDel(&report);
75 ajSeqallDel(&seqall);
76 ajSeqDel(&seq);
77
78 embExit();
79 return 0;
80 }
81