1 /* @source cutseq application
2 **
3 ** Removes a specified section from a sequence
4 **
5 ** @author Copyright (C) Gary Williams (gwilliam@hgmp.mrc.ac.uk)
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 cutseq ***************************************************************
29 **
30 ** Removes a specified section from a sequence
31 **
32 ******************************************************************************/
33
main(int argc,char ** argv)34 int main(int argc, char **argv)
35 {
36 AjPSeq seq;
37 AjPSeqout seqout;
38 ajint from;
39 ajint to;
40 AjPStr str = NULL;
41 ajint beg;
42 ajint end;
43
44 embInit("cutseq", argc, argv);
45
46 seq = ajAcdGetSeq("sequence");
47 from = ajAcdGetInt("from")-1;
48 to = ajAcdGetInt("to")-1;
49 seqout = ajAcdGetSeqout("outseq");
50
51 beg = ajSeqGetBegin(seq)-1;
52 end = ajSeqGetEnd(seq)-1;
53
54 str = ajStrNew();
55
56 /* get a COPY of the sequence string */
57 ajStrAssignSubS(&str, ajSeqGetSeqS(seq), beg, end);
58 ajStrCutRange(&str, from-beg, to-beg);
59
60 ajSeqAssignSeqS(seq, str);
61
62 ajSeqoutWriteSeq(seqout, seq);
63 ajSeqoutClose(seqout);
64
65 ajStrDel(&str);
66 ajSeqDel(&seq);
67 ajSeqoutDel(&seqout);
68
69 embExit();
70 return 0;
71 }
72