|
0
|
1 /******************************************************************************
|
|
|
2 ** @source gdinuc
|
|
|
3 **
|
|
|
4 ** Calculates dinucleotide usage
|
|
|
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 gdinuc ***************************************************************
|
|
|
35 **
|
|
|
36 ** Calculates dinucleotide usage
|
|
|
37 **
|
|
|
38 ******************************************************************************/
|
|
|
39
|
|
|
40 int main(int argc, char *argv[])
|
|
|
41 {
|
|
|
42 embInitPV("gdinuc", argc, argv, "GEMBASSY", "1.0.3");
|
|
|
43
|
|
|
44 AjPSeqall seqall;
|
|
|
45 AjPSeq seq;
|
|
|
46 AjPStr inseq = NULL;
|
|
|
47
|
|
|
48 AjBool translate = ajFalse;
|
|
|
49 AjPStr position = NULL;
|
|
|
50 AjPStr delkey = NULL;
|
|
|
51
|
|
|
52 AjBool accid = ajFalse;
|
|
|
53 AjPStr restid = NULL;
|
|
|
54 AjPStr seqid = NULL;
|
|
|
55
|
|
|
56 AjPStr base = NULL;
|
|
|
57 AjPStr url = NULL;
|
|
|
58
|
|
|
59 AjPFile tmpfile = NULL;
|
|
|
60 AjPStr tmpname = NULL;
|
|
|
61
|
|
|
62 AjPFile outf = NULL;
|
|
|
63
|
|
|
64 seqall = ajAcdGetSeqall("sequence");
|
|
|
65 translate = ajAcdGetBoolean("translate");
|
|
|
66 position = ajAcdGetListSingle("position");
|
|
|
67 delkey = ajAcdGetString("delkey");
|
|
|
68 accid = ajAcdGetBoolean("accid");
|
|
|
69 outf = ajAcdGetOutfile("outfile");
|
|
|
70
|
|
|
71 if(ajStrMatchCaseC(position, "all"))
|
|
|
72 {
|
|
|
73 ajStrDel(&position);
|
|
|
74 position = ajStrNew();
|
|
|
75 }
|
|
|
76
|
|
|
77 base = ajStrNewC("rest.g-language.org");
|
|
|
78
|
|
|
79 gAssignUniqueName(&tmpname);
|
|
|
80
|
|
|
81 while(ajSeqallNext(seqall, &seq))
|
|
|
82 {
|
|
|
83 inseq = NULL;
|
|
|
84
|
|
|
85 if(!accid)
|
|
|
86 {
|
|
|
87 if(gFormatGenbank(seq, &inseq))
|
|
|
88 {
|
|
|
89 tmpfile = ajFileNewOutNameS(tmpname);
|
|
|
90 if(!tmpfile)
|
|
|
91 {
|
|
|
92 ajDie("Output file (%S) open error\n", tmpname);
|
|
|
93 }
|
|
|
94 ajFmtPrintF(tmpfile, "%S", inseq);
|
|
|
95 ajFileClose(&tmpfile);
|
|
|
96 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
|
|
|
97 gFilePostSS(url, tmpname, &restid);
|
|
|
98 ajStrDel(&url);
|
|
|
99 ajSysFileUnlinkS(tmpname);
|
|
|
100 }
|
|
|
101 else
|
|
|
102 {
|
|
|
103 ajWarn("Sequence does not have features\n"
|
|
|
104 "Proceeding with sequence accession ID\n");
|
|
|
105 accid = ajTrue;
|
|
|
106 }
|
|
|
107 }
|
|
|
108
|
|
|
109 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
|
|
|
110
|
|
|
111 if(ajStrGetLen(seqid) == 0)
|
|
|
112 {
|
|
|
113 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
|
|
|
114 }
|
|
|
115
|
|
|
116 if(ajStrGetLen(seqid) == 0)
|
|
|
117 {
|
|
|
118 ajWarn("No valid header information\n");
|
|
|
119 }
|
|
|
120
|
|
|
121 if(accid)
|
|
|
122 {
|
|
|
123 ajStrAssignS(&restid, seqid);
|
|
|
124 if(ajStrGetLen(seqid) == 0)
|
|
|
125 {
|
|
|
126 ajDie("Cannot proceed without header with -accid\n");
|
|
|
127 }
|
|
|
128
|
|
|
129 if(!gValID(seqid))
|
|
|
130 {
|
|
|
131 ajDie("Invalid accession ID:%S, exiting\n", seqid);
|
|
|
132 }
|
|
|
133 }
|
|
|
134
|
|
|
135 url = ajStrNew();
|
|
|
136
|
|
|
137 ajFmtPrintS(&url, "http://%S/%S/dinuc/translate=%d/position=%S/"
|
|
|
138 "delkey=%S/output=f/tag=gene", base, restid, translate,
|
|
|
139 position, delkey);
|
|
|
140
|
|
|
141 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
|
|
|
142 if(!gFileOutURLS(url, &outf))
|
|
|
143 {
|
|
|
144 ajDie("Failed to download result from:\n%S\n", url);
|
|
|
145 }
|
|
|
146
|
|
|
147 ajStrDel(&url);
|
|
|
148 ajStrDel(&restid);
|
|
|
149 ajStrDel(&seqid);
|
|
|
150 ajStrDel(&inseq);
|
|
|
151 }
|
|
|
152
|
|
|
153 ajFileClose(&outf);
|
|
|
154
|
|
|
155 ajSeqallDel(&seqall);
|
|
|
156 ajSeqDel(&seq);
|
|
|
157 ajStrDel(&base);
|
|
|
158
|
|
|
159 ajStrDel(&position);
|
|
|
160 ajStrDel(&delkey);
|
|
|
161
|
|
|
162 embExit();
|
|
|
163
|
|
|
164 return 0;
|
|
|
165 }
|
