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comparison GEMBASSY-1.0.3/src/ggcwin.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 ggcwin
3 **
4 ** Calculates the GC content along the given genome
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 ggcwin ***************************************************************
36 **
37 ** Calculates the GC content along the given genome
38 **
39 ******************************************************************************/
40
41 int main(int argc, char *argv[])
42 {
43 embInitPV("ggcwin", argc, argv, "GEMBASSY", "1.0.3");
44
45 AjPSeqall seqall;
46 AjPSeq seq;
47 AjPStr inseq = NULL;
48
49 AjBool accid = ajFalse;
50 AjPStr restid = NULL;
51 AjPStr seqid = NULL;
52
53 AjPStr base = NULL;
54 AjPStr url = NULL;
55
56 AjPStr tmpname = NULL;
57 AjPSeqout tmpout = NULL;
58
59 ajint window = 0;
60 AjBool at = 0;
61 AjBool purine = 0;
62 AjBool keto = 0;
63
64 AjBool plot = 0;
65 AjPFile outf = NULL;
66 AjPFilebuff buff = NULL;
67 AjPGraph mult = NULL;
68
69 gPlotParams gpp;
70 AjPStr title = NULL;
71
72 seqall = ajAcdGetSeqall("sequence");
73 window = ajAcdGetInt("window");
74 at = ajAcdGetBoolean("at");
75 purine = ajAcdGetBoolean("purine");
76 keto = ajAcdGetBoolean("keto");
77
78 plot = ajAcdGetToggle("plot");
79 outf = ajAcdGetOutfile("outfile");
80 mult = ajAcdGetGraphxy("graph");
81
82 base = ajStrNewC("rest.g-language.org");
83
84 gAssignUniqueName(&tmpname);
85 ajStrAppendC(&tmpname, ".fasta");
86
87 while(ajSeqallNext(seqall, &seq))
88 {
89 tmpout = ajSeqoutNew();
90
91 if(!ajSeqoutOpenFilename(tmpout, tmpname))
92 {
93 embExitBad();
94 }
95
96 ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
97 ajSeqoutWriteSeq(tmpout, seq);
98 ajSeqoutClose(tmpout);
99 ajSeqoutDel(&tmpout);
100
101 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
102 gFilePostSS(url, tmpname, &restid);
103 ajStrDel(&url);
104 ajSysFileUnlinkS(tmpname);
105
106 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
107
108 if(ajStrGetLen(seqid) == 0)
109 {
110 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
111 }
112
113 if(ajStrGetLen(seqid) == 0)
114 {
115 ajWarn("No valid header information\n");
116 }
117
118 url = ajStrNew();
119
120 ajFmtPrintS(&url, "http://%S/%S/gcwin/window=%d/at=%d/purine=%d/"
121 "keto=%d/output=f/", base, restid, window, at, purine, keto);
122
123 if(plot)
124 {
125 title = ajStrNew();
126
127 ajStrAppendC(&title, argv[0]);
128 ajStrAppendC(&title, " of ");
129 ajStrAppendS(&title, seqid);
130
131 gpp.title = ajStrNewS(title);
132 gpp.xlab = ajStrNewC("location");
133 gpp.ylab = ajStrNewC("GC content");
134
135 if(!gFilebuffURLS(url, &buff))
136 {
137 ajDie("File downloading error from:\n%S\n", url);
138 }
139
140 if(!gPlotFilebuff(buff, mult, &gpp))
141 {
142 ajDie("Error in plotting\n");
143 }
144
145 AJFREE(gpp.title);
146 AJFREE(gpp.xlab);
147 AJFREE(gpp.ylab);
148 ajStrDel(&title);
149 ajFilebuffDel(&buff);
150 }
151 else
152 {
153 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
154 if(!gFileOutURLS(url, &outf))
155 {
156 ajDie("File downloading error from:\n%S\n", url);
157 }
158 }
159 ajStrDel(&url);
160 ajStrDel(&restid);
161 ajStrDel(&seqid);
162 }
163
164 ajFileClose(&outf);
165
166 ajSeqallDel(&seqall);
167 ajSeqDel(&seq);
168 ajStrDel(&base);
169
170 embExit();
171
172 return 0;
173 }