comparison GEMBASSY-1.0.3/src/gfindoriter.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 gfindoriter
3 **
4 ** Predict the replication origin and terminus in bacterial genomes
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 gfindoriter ********************************************************
36 **
37 ** Predict the replication origin and terminus in bacterial genomes
38 **
39 ******************************************************************************/
40
41 int main(int argc, char *argv[])
42 {
43 embInitPV("gfindoriter", argc, argv, "GEMBASSY", "1.0.3");
44
45 AjPSeqall seqall;
46 AjPSeq seq;
47
48 ajint window = 0;
49 AjBool purine = 0;
50 AjBool keto = 0;
51 ajint lowpass = 0;
52
53 AjPStr ori = NULL;
54 AjPStr ter = NULL;
55
56 AjPStr restid = NULL;
57 AjPStr seqid = NULL;
58
59 AjPStr base = NULL;
60 AjPStr url = NULL;
61
62 AjPStr tmpname = NULL;
63 AjPSeqout tmpout = NULL;
64 AjPFilebuff tmpbuff = NULL;
65
66 AjPStr tmp = NULL;
67 AjPStr line = NULL;
68
69 AjPRegexp regex;
70
71 AjPFile outf = NULL;
72
73 seqall = ajAcdGetSeqall("sequence");
74 window = ajAcdGetInt("window");
75 lowpass = ajAcdGetInt("lowpass");
76 purine = ajAcdGetBoolean("purine");
77 keto = ajAcdGetBoolean("keto");
78 outf = ajAcdGetOutfile("outfile");
79
80 base = ajStrNewC("rest.g-language.org");
81
82 gAssignUniqueName(&tmpname);
83 ajStrAppendC(&tmpname, ".fasta");
84
85 while(ajSeqallNext(seqall, &seq))
86 {
87 tmpout = ajSeqoutNew();
88
89 if(!ajSeqoutOpenFilename(tmpout, tmpname))
90 {
91 embExitBad();
92 }
93
94 ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
95 ajSeqoutWriteSeq(tmpout, seq);
96 ajSeqoutClose(tmpout);
97 ajSeqoutDel(&tmpout);
98
99 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
100 gFilePostSS(url, tmpname, &restid);
101 ajStrDel(&url);
102 ajSysFileUnlinkS(tmpname);
103
104 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
105
106 if(ajStrGetLen(seqid) == 0)
107 {
108 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
109 }
110
111 if(ajStrGetLen(seqid) == 0)
112 {
113 ajWarn("No valid header information\n");
114 }
115
116 url = ajStrNew();
117
118 ajFmtPrintS(&url, "http://%S/%S/find_ori_ter/window=%d/lowpass=%d/"
119 "purine=%d/keto=%d/", base, restid, window, lowpass,
120 purine, keto);
121
122 if(!gFilebuffURLS(url, &tmpbuff))
123 {
124 ajDie("Failed to download result from:\n%S\n", url);
125 }
126
127 regex = ajRegCompC("([0-9]+)$");
128
129 while(ajBuffreadLine(tmpbuff, &line))
130 {
131 if(ajRegExec(regex, line))
132 {
133 if(ajRegSubI(regex, 0, &tmp))
134 {
135 if(ajStrGetLen(ori) == 0)
136 {
137 ajStrAssignS(&ori, tmp);
138 }
139 else if(ajStrGetLen(ter) == 0)
140 {
141 ajStrAssignS(&ter, tmp);
142 }
143 }
144 }
145 }
146
147 ajFmtPrintF(outf, "Sequence: %S Origin: %S Terminus: %S\n",
148 seqid, ori, ter);
149
150 ajStrDel(&tmp);
151 ajStrDel(&ori);
152 ajStrDel(&ter);
153
154 ajStrDel(&url);
155 ajStrDel(&restid);
156 }
157
158 ajFileClose(&outf);
159
160 ajSeqallDel(&seqall);
161 ajSeqDel(&seq);
162 ajStrDel(&seqid);
163
164 embExit();
165
166 return 0;
167 }