|
0
|
1 /******************************************************************************
|
|
|
2 ** @source gsvalue
|
|
|
3 **
|
|
|
4 ** Calculate the strength of selected codon usage 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 Refactor
|
|
|
11 ** @@
|
|
|
12 **
|
|
|
13 ** This program is free software; you can redistribute it and/or
|
|
|
14 ** modify it under the terms of the GNU General Public License
|
|
|
15 ** as published by the Free Software Foundation; either version 2
|
|
|
16 ** of the License, or (at your option) any later version.
|
|
|
17 **
|
|
|
18 ** This program is distributed in the hope that it will be useful,
|
|
|
19 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
|
20 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
|
21 ** GNU General Public License for more details.
|
|
|
22 **
|
|
|
23 ** You should have received a copy of the GNU General Public License
|
|
|
24 ** along with this program; if not, write to the Free Software
|
|
|
25 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
|
|
|
26 ******************************************************************************/
|
|
|
27
|
|
|
28 #include "emboss.h"
|
|
|
29 #include "glibs.h"
|
|
|
30
|
|
|
31
|
|
|
32
|
|
|
33
|
|
|
34 /* @prog gsvalue **************************************************************
|
|
|
35 **
|
|
|
36 ** Calculate the strength of selected codon usage bias
|
|
|
37 **
|
|
|
38 ******************************************************************************/
|
|
|
39
|
|
|
40 int main(int argc, char *argv[])
|
|
|
41 {
|
|
|
42 embInitPV("gsvalue", argc, argv, "GEMBASSY", "1.0.3");
|
|
|
43
|
|
|
44 AjPSeqall seqall;
|
|
|
45 AjPSeq seq;
|
|
|
46 AjPStr inseq = NULL;
|
|
|
47
|
|
|
48 AjBool sharp = ajFalse;
|
|
|
49
|
|
|
50 AjBool accid = ajFalse;
|
|
|
51 AjPStr restid = NULL;
|
|
|
52 AjPStr seqid = NULL;
|
|
|
53
|
|
|
54 AjPStr base = NULL;
|
|
|
55 AjPStr url = NULL;
|
|
|
56
|
|
|
57 AjPFile tmpfile = NULL;
|
|
|
58 AjPStr tmpname = NULL;
|
|
|
59
|
|
|
60 AjPFilebuff tmp = NULL;
|
|
|
61 AjPStr line = NULL;
|
|
|
62
|
|
|
63 AjPFile outf = NULL;
|
|
|
64
|
|
|
65 seqall = ajAcdGetSeqall("sequence");
|
|
|
66 sharp = ajAcdGetBoolean("sharp");
|
|
|
67 accid = ajAcdGetBoolean("accid");
|
|
|
68 outf = ajAcdGetOutfile("outfile");
|
|
|
69
|
|
|
70 base = ajStrNewC("rest.g-language.org");
|
|
|
71
|
|
|
72 gAssignUniqueName(&tmpname);
|
|
|
73
|
|
|
74 while(ajSeqallNext(seqall, &seq))
|
|
|
75 {
|
|
|
76 inseq = NULL;
|
|
|
77
|
|
|
78 if(!accid)
|
|
|
79 {
|
|
|
80 if(gFormatGenbank(seq, &inseq))
|
|
|
81 {
|
|
|
82 tmpfile = ajFileNewOutNameS(tmpname);
|
|
|
83 if(!tmpfile)
|
|
|
84 {
|
|
|
85 ajDie("Output file (%S) open error\n", tmpname);
|
|
|
86 }
|
|
|
87 ajFmtPrintF(tmpfile, "%S", inseq);
|
|
|
88 ajFileClose(&tmpfile);
|
|
|
89 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
|
|
|
90 gFilePostSS(url, tmpname, &restid);
|
|
|
91 ajStrDel(&url);
|
|
|
92 ajSysFileUnlinkS(tmpname);
|
|
|
93 }
|
|
|
94 else
|
|
|
95 {
|
|
|
96 ajWarn("Sequence does not have features\n"
|
|
|
97 "Proceeding with sequence accession ID\n");
|
|
|
98 accid = ajTrue;
|
|
|
99 }
|
|
|
100 }
|
|
|
101
|
|
|
102 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
|
|
|
103
|
|
|
104 if(ajStrGetLen(seqid) == 0)
|
|
|
105 {
|
|
|
106 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
|
|
|
107 }
|
|
|
108
|
|
|
109 if(ajStrGetLen(seqid) == 0)
|
|
|
110 {
|
|
|
111 ajWarn("No valid header information\n");
|
|
|
112 }
|
|
|
113
|
|
|
114 if(accid)
|
|
|
115 {
|
|
|
116 ajStrAssignS(&restid, seqid);
|
|
|
117 if(ajStrGetLen(seqid) == 0)
|
|
|
118 {
|
|
|
119 ajDie("Cannot proceed without header with -accid\n");
|
|
|
120 }
|
|
|
121
|
|
|
122 if(!gValID(seqid))
|
|
|
123 {
|
|
|
124 ajDie("Invalid accession ID:%S, exiting\n", seqid);
|
|
|
125 }
|
|
|
126 }
|
|
|
127
|
|
|
128 url = ajStrNew();
|
|
|
129
|
|
|
130 ajFmtPrintS(&url, "http://%S/%S/S_value/sharp=%d/output=f/tag=gene",
|
|
|
131 base, restid, sharp);
|
|
|
132
|
|
|
133 if(!gFilebuffURLS(url, &tmp))
|
|
|
134 {
|
|
|
135 ajDie("Failed to download result from:\n%S\n", url);
|
|
|
136 }
|
|
|
137
|
|
|
138 ajBuffreadLine(tmp, &line);
|
|
|
139
|
|
|
140 ajStrRemoveSetC(&line, "\n");
|
|
|
141
|
|
|
142 ajFmtPrintF(outf, "Sequence: %S S-value: %S\n", seqid, line);
|
|
|
143
|
|
|
144 ajStrDel(&url);
|
|
|
145 ajStrDel(&restid);
|
|
|
146 ajStrDel(&seqid);
|
|
|
147 ajStrDel(&inseq);
|
|
|
148 }
|
|
|
149
|
|
|
150 ajFileClose(&outf);
|
|
|
151
|
|
|
152 ajSeqallDel(&seqall);
|
|
|
153 ajSeqDel(&seq);
|
|
|
154 ajStrDel(&base);
|
|
|
155
|
|
|
156 embExit();
|
|
|
157
|
|
|
158 return 0;
|
|
|
159 }
|
