|
0
|
1 /******************************************************************************
|
|
|
2 ** @source greporiter
|
|
|
3 **
|
|
|
4 ** Get the positions of replication origin and terminus
|
|
|
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 greporiter *********************************************************
|
|
|
36 **
|
|
|
37 ** Get the positions of replication origin and terminus
|
|
|
38 **
|
|
|
39 ******************************************************************************/
|
|
|
40
|
|
|
41 int main(int argc, char *argv[])
|
|
|
42 {
|
|
|
43 embInitPV("greporiter", 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 AjBool oriloc = 0;
|
|
|
57 AjBool gcskew = 0;
|
|
|
58 AjBool dbonly = 0;
|
|
|
59 ajint difthreshold = 0;
|
|
|
60
|
|
|
61 AjPFile outf = NULL;
|
|
|
62
|
|
|
63 AjPFile tmpfile = NULL;
|
|
|
64 AjPStr tmpname = NULL;
|
|
|
65 AjPStr fstname = NULL;
|
|
|
66 AjPFilebuff tmp = NULL;
|
|
|
67 AjPStr line = NULL;
|
|
|
68 AjPSeqout tmpout = NULL;
|
|
|
69
|
|
|
70 AjPRegexp regex;
|
|
|
71
|
|
|
72 AjPStr ori = NULL;
|
|
|
73 AjPStr ter = NULL;
|
|
|
74
|
|
|
75 seqall = ajAcdGetSeqall("sequence");
|
|
|
76 difthreshold = ajAcdGetInt("difthreshold");
|
|
|
77 oriloc = ajAcdGetBoolean("oriloc");
|
|
|
78 gcskew = ajAcdGetBoolean("gcskew");
|
|
|
79 dbonly = ajAcdGetBoolean("dbonly");
|
|
|
80 accid = ajAcdGetBoolean("accid");
|
|
|
81 outf = ajAcdGetOutfile("outfile");
|
|
|
82
|
|
|
83 base = ajStrNewC("rest.g-language.org");
|
|
|
84
|
|
|
85 gAssignUniqueName(&tmpname);
|
|
|
86 gAssignUniqueName(&fstname);
|
|
|
87 ajStrAppendC(&fstname, ".fasta");
|
|
|
88
|
|
|
89 while(ajSeqallNext(seqall, &seq))
|
|
|
90 {
|
|
|
91 inseq = ajStrNew();
|
|
|
92
|
|
|
93 tmpout = ajSeqoutNew();
|
|
|
94
|
|
|
95 if(!accid)
|
|
|
96 {
|
|
|
97 if(gFormatGenbank(seq, &inseq))
|
|
|
98 {
|
|
|
99 tmpfile = ajFileNewOutNameS(tmpname);
|
|
|
100 if(!tmpfile)
|
|
|
101 {
|
|
|
102 ajDie("Output file (%S) open error\n", tmpname);
|
|
|
103 }
|
|
|
104 ajFmtPrintF(tmpfile, "%S", inseq);
|
|
|
105 ajFileClose(&tmpfile);
|
|
|
106 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
|
|
|
107 gFilePostSS(url, tmpname, &restid);
|
|
|
108 ajStrDel(&url);
|
|
|
109 ajSysFileUnlinkS(tmpname);
|
|
|
110 }
|
|
|
111 else
|
|
|
112 {
|
|
|
113 if(!ajSeqoutOpenFilename(tmpout, fstname))
|
|
|
114 {
|
|
|
115 embExitBad();
|
|
|
116 }
|
|
|
117
|
|
|
118 ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
|
|
|
119 ajSeqoutWriteSeq(tmpout, seq);
|
|
|
120 ajSeqoutClose(tmpout);
|
|
|
121 ajSeqoutDel(&tmpout);
|
|
|
122 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
|
|
|
123 gFilePostSS(url, fstname, &restid);
|
|
|
124 ajStrDel(&url);
|
|
|
125 ajSysFileUnlinkS(fstname);
|
|
|
126 }
|
|
|
127 }
|
|
|
128
|
|
|
129 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
|
|
|
130
|
|
|
131 if(ajStrGetLen(seqid) == 0)
|
|
|
132 {
|
|
|
133 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
|
|
|
134 }
|
|
|
135
|
|
|
136 if(ajStrGetLen(seqid) == 0)
|
|
|
137 {
|
|
|
138 ajWarn("No valid header information\n");
|
|
|
139 }
|
|
|
140
|
|
|
141 if(accid)
|
|
|
142 {
|
|
|
143 ajStrAssignS(&restid, seqid);
|
|
|
144 if(ajStrGetLen(seqid) == 0)
|
|
|
145 {
|
|
|
146 ajDie("Cannot proceed without header with -accid\n");
|
|
|
147 }
|
|
|
148
|
|
|
149 if(!gValID(seqid))
|
|
|
150 {
|
|
|
151 ajDie("Invalid accession ID:%S, exiting\n", seqid);
|
|
|
152 }
|
|
|
153 }
|
|
|
154
|
|
|
155 url = ajStrNew();
|
|
|
156
|
|
|
157 ajFmtPrintS(&url, "http://%S/%S/rep_ori_ter/oriloc=%d/gcskew=%d/"
|
|
|
158 "difthreshold=%d/dbonly=%d/", base, restid, oriloc, gcskew,
|
|
|
159 difthreshold, dbonly);
|
|
|
160
|
|
|
161 if(!gFilebuffURLS(url, &tmp))
|
|
|
162 {
|
|
|
163 ajDie("Failed to download result from:\n%S\n", url);
|
|
|
164 }
|
|
|
165
|
|
|
166 ajBuffreadLine(tmp, &line);
|
|
|
167
|
|
|
168 regex = ajRegCompC("([0-9]+),([0-9]+)");
|
|
|
169
|
|
|
170 if(ajRegExec(regex, line)) {
|
|
|
171 if(ajRegSubI(regex, 1, &ori), ajRegSubI(regex, 2, &ter)) {
|
|
|
172 ajFmtPrint("%S Origin: %S Terminus %S\n", seqid, ori, ter);
|
|
|
173 }
|
|
|
174 }
|
|
|
175
|
|
|
176 ajStrDel(&url);
|
|
|
177 ajStrDel(&restid);
|
|
|
178 ajStrDel(&seqid);
|
|
|
179 ajStrDel(&inseq);
|
|
|
180 }
|
|
|
181
|
|
|
182 ajFileClose(&outf);
|
|
|
183
|
|
|
184 ajSeqallDel(&seqall);
|
|
|
185 ajSeqDel(&seq);
|
|
|
186 ajStrDel(&base);
|
|
|
187
|
|
|
188 embExit();
|
|
|
189
|
|
|
190 return 0;
|
|
|
191 }
|
