1 /* @source geecee application
2 **
3 ** Get GC content
4 **
5 ** @author Copyright (C) Richard Bruskievich
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 geecee ***************************************************************
29 **
30 ** Calculates the fractional GC content of nucleic acid sequences
31 **
32 ******************************************************************************/
33
main(int argc,char ** argv)34 int main(int argc, char **argv)
35 {
36
37 AjPSeq seq;
38 AjPSeqall seqall;
39 const AjPStr seqstr;
40 AjPFile outf;
41 ajint len;
42 float pgc;
43
44 embInit("geecee", argc, argv);
45
46 seqall = ajAcdGetSeqall("sequence");
47 outf = ajAcdGetOutfile("outfile");
48
49 ajFmtPrintF(outf, "#Sequence GC content\n");
50 while(ajSeqallNext(seqall, &seq))
51 {
52 ajSeqTrim(seq);
53 seqstr = ajSeqGetSeqS(seq);
54 len = ajSeqGetLen(seq);
55 pgc = ajMeltGC(seqstr,len); /* forward strand for now... */
56
57 ajFmtPrintF(outf, "%-12s %5.2f\n", ajSeqGetNameC(seq), pgc);
58 }
59
60 ajSeqallDel(&seqall);
61 ajSeqDel(&seq);
62
63 ajFileClose(&outf);
64
65 embExit();
66
67 return 0;
68 }
69