|
0
|
1 /******************************************************************************
|
|
|
2 ** @source gaminoinfo
|
|
|
3 **
|
|
|
4 ** Prints out basic amino acid sequence statistics
|
|
|
5 **
|
|
|
6 ** @author Copyright (C) 2012 Hidetoshi Itaya
|
|
|
7 ** @version 1.0.3
|
|
|
8 ** @modified 2012/1/20 Hidetoshi Itaya Created!
|
|
|
9 ** @modified 2013/6/16 Revision 1
|
|
|
10 ** @modified 2015/2/7 Refactor
|
|
|
11 ** @@
|
|
|
12 **
|
|
|
13 ** This program is free software; you can redistribute it and/or
|
|
|
14 ** modify it under the terms of the GNU General Public License
|
|
|
15 ** as published by the Free Software Foundation; either version 2
|
|
|
16 ** of the License, or (at your option) any later version.
|
|
|
17 **
|
|
|
18 ** This program is distributed in the hope that it will be useful,
|
|
|
19 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
|
20 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
|
21 ** GNU General Public License for more details.
|
|
|
22 **
|
|
|
23 ** You should have received a copy of the GNU General Public License
|
|
|
24 ** along with this program; if not, write to the Free Software
|
|
|
25 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
|
|
|
26 ******************************************************************************/
|
|
|
27
|
|
|
28 #include "emboss.h"
|
|
|
29 #include "glibs.h"
|
|
|
30
|
|
|
31
|
|
|
32
|
|
|
33
|
|
|
34 /* @prog gaminoinfo ***********************************************************
|
|
|
35 **
|
|
|
36 ** Prints out basic amino acid sequence statisctics
|
|
|
37 **
|
|
|
38 ******************************************************************************/
|
|
|
39
|
|
|
40 int main(int argc, char *argv[])
|
|
|
41 {
|
|
|
42 embInitPV("gaminoinfo", argc, argv, "GEMBASSY", "1.0.3");
|
|
|
43
|
|
|
44 AjPSeqall seqall;
|
|
|
45 AjPSeq seq;
|
|
|
46
|
|
|
47 AjPStr restid = NULL;
|
|
|
48 AjPStr seqid = NULL;
|
|
|
49
|
|
|
50 AjPStr base = NULL;
|
|
|
51 AjPStr url = NULL;
|
|
|
52
|
|
|
53 AjPStr tmpname = NULL;
|
|
|
54 AjPSeqout tmpout = NULL;
|
|
|
55
|
|
|
56 AjPFile outf = NULL;
|
|
|
57
|
|
|
58 seqall = ajAcdGetSeqall("sequence");
|
|
|
59 outf = ajAcdGetOutfile("outfile");
|
|
|
60
|
|
|
61 base = ajStrNewC("rest.g-language.org");
|
|
|
62
|
|
|
63 gAssignUniqueName(&tmpname);
|
|
|
64 ajStrAppendC(&tmpname, ".fasta");
|
|
|
65
|
|
|
66 while(ajSeqallNext(seqall, &seq))
|
|
|
67 {
|
|
|
68 tmpout = ajSeqoutNew();
|
|
|
69
|
|
|
70 if(!ajSeqoutOpenFilename(tmpout, tmpname))
|
|
|
71 {
|
|
|
72 embExitBad();
|
|
|
73 }
|
|
|
74
|
|
|
75 ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
|
|
|
76 ajSeqoutWriteSeq(tmpout, seq);
|
|
|
77 ajSeqoutClose(tmpout);
|
|
|
78 ajSeqoutDel(&tmpout);
|
|
|
79
|
|
|
80 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
|
|
|
81 gFilePostSS(url, tmpname, &restid);
|
|
|
82 ajStrDel(&url);
|
|
|
83 ajSysFileUnlinkS(tmpname);
|
|
|
84
|
|
|
85 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
|
|
|
86
|
|
|
87 if(ajStrGetLen(seqid) == 0)
|
|
|
88 {
|
|
|
89 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
|
|
|
90 }
|
|
|
91
|
|
|
92 if(ajStrGetLen(seqid) == 0)
|
|
|
93 {
|
|
|
94 ajWarn("No valid header information\n");
|
|
|
95 }
|
|
|
96
|
|
|
97 url = ajStrNew();
|
|
|
98
|
|
|
99 ajFmtPrintS(&url, "http://%S/%S/amino_info", base, restid);
|
|
|
100
|
|
|
101 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
|
|
|
102 if(!gFileOutURLS(url, &outf))
|
|
|
103 {
|
|
|
104 ajDie("Failed to download result from:\n%S\n", url);
|
|
|
105 }
|
|
|
106
|
|
|
107 ajStrDel(&url);
|
|
|
108 ajStrDel(&restid);
|
|
|
109 ajStrDel(&seqid);
|
|
|
110 }
|
|
|
111
|
|
|
112 ajFileClose(&outf);
|
|
|
113
|
|
|
114 ajSeqallDel(&seqall);
|
|
|
115 ajSeqDel(&seq);
|
|
|
116 ajStrDel(&base);
|
|
|
117
|
|
|
118 embExit();
|
|
|
119
|
|
|
120 return 0;
|
|
|
121 }
|
