comparison GEMBASSY-1.0.3/src/ggcsi.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 ggcsi
3 **
4 ** GC Skew Index: an index for strand-specific mutational bias
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 RESTify
11 ** @modified 2015/2/7 Refactor
12 ** @@
13 **
14 ** This program is free software; you can redistribute it and/or
15 ** modify it under the terms of the GNU General Public License
16 ** as published by the Free Software Foundation; either version 2
17 ** of the License, or (at your option) any later version.
18 **
19 ** This program is distributed in the hope that it will be useful,
20 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
21 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22 ** GNU General Public License for more details.
23 **
24 ** You should have received a copy of the GNU General Public License
25 ** along with this program; if not, write to the Free Software
26 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
27 ******************************************************************************/
28
29 #include "emboss.h"
30 #include "glibs.h"
31
32
33
34
35 /* @prog ggcsi ****************************************************************
36 **
37 ** GC Skew Index: an index for strand-specific mutational bias
38 **
39 ******************************************************************************/
40
41 int main(int argc, char *argv[])
42 {
43 embInitPV("ggcsi", argc, argv, "GEMBASSY", "1.0.3");
44
45 AjPSeqall seqall;
46 AjPSeq seq;
47 AjPStr inseq = NULL;
48
49 AjPStr restid = NULL;
50 AjPStr seqid = NULL;
51
52 AjPStr base = NULL;
53 AjPStr url = NULL;
54
55 ajint window = 0;
56 AjBool at = 0;
57 AjBool purine = 0;
58 AjBool keto = 0;
59 AjBool pval = 0;
60 AjPStr version = NULL;
61
62 AjPStr tmpname = NULL;
63 AjPSeqout tmpout = NULL;
64 AjPFilebuff tmpbuff = NULL;
65
66 AjPStr tmp = NULL;
67 AjPStr parse = NULL;
68 AjPStr gcsi = NULL;
69 AjPStr sa = NULL;
70 AjPStr dist = NULL;
71 AjPStr z = NULL;
72 AjPStr p = NULL;
73
74 AjPStrTok handle = NULL;
75
76 AjPFile outf = NULL;
77
78 seqall = ajAcdGetSeqall("sequence");
79 window = ajAcdGetInt("window");
80 at = ajAcdGetBoolean("at");
81 purine = ajAcdGetBoolean("purine");
82 keto = ajAcdGetBoolean("keto");
83 pval = ajAcdGetBoolean("pval");
84 version = ajAcdGetSelectSingle("gcsi");
85 outf = ajAcdGetOutfile("outfile");
86
87 base = ajStrNewC("rest.g-language.org");
88
89 gAssignUniqueName(&tmpname);
90 ajStrAppendC(&tmpname, ".fasta");
91
92 while(ajSeqallNext(seqall, &seq))
93 {
94 tmpout = ajSeqoutNew();
95
96 if(!ajSeqoutOpenFilename(tmpout, tmpname))
97 {
98 embExitBad();
99 }
100
101 ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
102 ajSeqoutWriteSeq(tmpout, seq);
103 ajSeqoutClose(tmpout);
104 ajSeqoutDel(&tmpout);
105
106 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
107 gFilePostSS(url, tmpname, &restid);
108 ajStrDel(&url);
109 ajSysFileUnlinkS(tmpname);
110
111 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
112
113 if(ajStrGetLen(seqid) == 0)
114 {
115 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
116 }
117
118 if(ajStrGetLen(seqid) == 0)
119 {
120 ajWarn("No valid header information\n");
121 }
122
123 url = ajStrNew();
124
125 ajFmtPrintS(&url, "http://%S/%S/gcsi/window=%d/at=%d/purine=%d/"
126 "keto=%d/p=%d/version=%d/", base, restid, window, at, purine,
127 keto, pval, version);
128
129 if(!gFilebuffURLS(url, &tmpbuff))
130 {
131 ajDie("Failed to download result from:\n%S\n", url);
132 }
133
134 ajBuffreadLine(tmpbuff, &tmp);
135
136 parse = ajStrNew();
137 gcsi = ajStrNew();
138 sa = ajStrNew();
139 dist = ajStrNew();
140 z = ajStrNew();
141 p = ajStrNew();
142
143 ajStrRemoveLastNewline(&tmp);
144
145 handle = ajStrTokenNewC(tmp, ",");
146
147 while (ajStrTokenNextParse(handle, &parse))
148 {
149 if (ajStrIsFloat(parse))
150 {
151 if(!ajStrGetLen(gcsi))
152 ajStrAssignS(&gcsi, parse);
153 else if(!ajStrGetLen(sa))
154 ajStrAssignS(&sa, parse);
155 else if(!ajStrGetLen(dist))
156 ajStrAssignS(&dist, parse);
157 else if(!ajStrGetLen(z))
158 ajStrAssignS(&z, parse);
159 else if(!ajStrGetLen(p))
160 ajStrAssignS(&p, parse);
161 }
162 }
163
164 tmp = ajFmtStr("Sequence: %S GCSI: %S SA: %S DIST: %S",
165 seqid, gcsi, sa, dist);
166
167 if(pval)
168 tmp = ajFmtStr("%S Z: %S P: %S", tmp, z, p);
169
170 ajFmtPrintF(outf, "%S\n", tmp);
171
172 ajStrDel(&tmp);
173 ajStrDel(&parse);
174 ajStrDel(&gcsi);
175 ajStrDel(&sa);
176 ajStrDel(&dist);
177 ajStrDel(&z);
178 ajStrDel(&p);
179
180 ajStrDel(&inseq);
181 }
182
183 ajFileClose(&outf);
184
185 ajSeqallDel(&seqall);
186 ajSeqDel(&seq);
187 ajStrDel(&seqid);
188
189 embExit();
190
191 return 0;
192 }