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comparison GEMBASSY-1.0.3/src/gdinuc.c @ 0:8300eb051bea draft

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Initial upload
author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
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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 }