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comparison GEMBASSY-1.0.3/src/goligomersearch.c @ 2:8947fca5f715 draft default tip

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author ktnyt
date Fri, 26 Jun 2015 05:21:44 -0400
parents 84a17b3fad1f
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1:84a17b3fad1f 2:8947fca5f715
1 /******************************************************************************
2 ** @source goligomersearch
3 **
4 ** Counts the number of given oligomers in a sequence
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 goligomersearch ******************************************************
35 **
36 ** Counts the number of given oligomers in a sequence
37 **
38 ******************************************************************************/
39
40 int main(int argc, char *argv[])
41 {
42 embInitPV("goligomersearch", argc, argv, "GEMBASSY", "1.0.3");
43
44 AjPSeqall seqall;
45 AjPSeq seq;
46 AjPStr inseq = NULL;
47 AjPStr oligomer = NULL;
48
49 AjPStr restid = NULL;
50 AjPStr seqid = NULL;
51
52 AjPStr base = NULL;
53 AjPStr url = NULL;
54
55 AjPStr _return = NULL;
56
57 AjPStr tmpname = NULL;
58 AjPSeqout tmpout = NULL;
59
60 AjPFilebuff tmp = NULL;
61 AjPStr line = NULL;
62
63 AjPFile outfile = NULL;
64
65 seqall = ajAcdGetSeqall("sequence");
66 oligomer = ajAcdGetString("oligomer");
67 _return = ajAcdGetSelectSingle("return");
68 outfile = ajAcdGetOutfile("outfile");
69
70 base = ajStrNewC("rest.g-language.org");
71
72 gAssignUniqueName(&tmpname);
73 ajStrAppendC(&tmpname, ".fasta");
74
75 while(ajSeqallNext(seqall, &seq))
76 {
77 inseq = NULL;
78
79 tmpout = ajSeqoutNew();
80
81 if(!ajSeqoutOpenFilename(tmpout, tmpname))
82 {
83 embExitBad();
84 }
85
86 ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
87 ajSeqoutWriteSeq(tmpout, seq);
88 ajSeqoutClose(tmpout);
89 ajSeqoutDel(&tmpout);
90
91 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
92 gFilePostSS(url, tmpname, &restid);
93 ajStrDel(&url);
94 ajSysFileUnlinkS(tmpname);
95
96 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
97
98 if(ajStrGetLen(seqid) == 0)
99 {
100 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
101 }
102
103 if(ajStrGetLen(seqid) == 0)
104 {
105 ajWarn("No valid header information\n");
106 }
107
108 url = ajStrNew();
109
110 ajFmtPrintS(&url, "http://%S/%S/oligomer_search/%S/return=%S",
111 base, restid, oligomer, _return);
112
113 if(!gFilebuffURLS(url, &tmp))
114 {
115 ajDie("Failed to download result from:\n%S\n", url);
116 }
117
118 ajBuffreadLine(tmp, &line);
119
120 ajStrRemoveSetC(&line, "\n");
121
122 ajFmtPrintF(outfile, "Sequence: %S Oligomer: %S Return: %S\n",
123 seqid, oligomer, line);
124
125 ajStrDel(&url);
126 ajStrDel(&restid);
127 ajStrDel(&seqid);
128 ajStrDel(&inseq);
129 }
130
131 ajFileClose(&outfile);
132
133 ajSeqallDel(&seqall);
134 ajSeqDel(&seq);
135 ajStrDel(&base);
136
137 ajStrDel(&oligomer);
138
139 embExit();
140
141 return 0;
142 }