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comparison GEMBASSY-1.0.3/src/greporiter.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 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 }