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comparison GEMBASSY-1.0.3/src/gew.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 gew
3 **
4 ** Calculate a measure of synonymous codon usage evenness (Ew)
5 **
6 ** @author Copyright (C) 2012 Hidetoshi Itaya
7 ** @version 1.0.3 Revision 1
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 gew ******************************************************************
35 **
36 ** Calculate a measure of synonymous codon usage evenness (Ew)
37 **
38 ******************************************************************************/
39
40 int main(int argc, char *argv[])
41 {
42 embInitPV("gew", argc, argv, "GEMBASSY", "1.0.3");
43
44 AjPSeqall seqall;
45 AjPSeq seq;
46 AjPStr inseq = NULL;
47
48 AjBool translate = ajFalse;
49 AjPStr delkey = NULL;
50
51 AjBool accid = ajFalse;
52 AjPStr restid = NULL;
53 AjPStr seqid = NULL;
54
55 AjPStr base = NULL;
56 AjPStr url = NULL;
57
58 AjPFile tmpfile = NULL;
59 AjPStr tmpname = NULL;
60
61 AjPFile outf = NULL;
62
63 seqall = ajAcdGetSeqall("sequence");
64 translate = ajAcdGetBoolean("translate");
65 delkey = ajAcdGetString("delkey");
66 accid = ajAcdGetBoolean("accid");
67 outf = ajAcdGetOutfile("outfile");
68
69 base = ajStrNewC("rest.g-language.org");
70
71 gAssignUniqueName(&tmpname);
72
73 while(ajSeqallNext(seqall, &seq))
74 {
75 inseq = NULL;
76
77 if(!accid)
78 {
79 if(gFormatGenbank(seq, &inseq))
80 {
81 tmpfile = ajFileNewOutNameS(tmpname);
82 if(!tmpfile)
83 {
84 ajDie("Output file (%S) open error\n", tmpname);
85 }
86 ajFmtPrintF(tmpfile, "%S", inseq);
87 ajFileClose(&tmpfile);
88 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
89 gFilePostSS(url, tmpname, &restid);
90 ajStrDel(&url);
91 ajSysFileUnlinkS(tmpname);
92 }
93 else
94 {
95 ajWarn("Sequence does not have features\n"
96 "Proceeding with sequence accession ID\n");
97 accid = ajTrue;
98 }
99 }
100
101 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
102
103 if(ajStrGetLen(seqid) == 0)
104 {
105 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
106 }
107
108 if(ajStrGetLen(seqid) == 0)
109 {
110 ajWarn("No valid header information\n");
111 }
112
113 if(accid)
114 {
115 ajStrAssignS(&restid, seqid);
116 if(ajStrGetLen(seqid) == 0)
117 {
118 ajDie("Cannot proceed without header with -accid\n");
119 }
120
121 if(!gValID(seqid))
122 {
123 ajDie("Invalid accession ID:%S, exiting\n", seqid);
124 }
125 }
126
127 url = ajStrNew();
128
129 ajFmtPrintS(&url, "http://%S/%S/Ew/translate=%d/delkey=%S/"
130 "output=f/tag=gene", base, restid, translate, delkey);
131
132 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
133 if(!gFileOutURLS(url, &outf))
134 {
135 ajDie("Failed to download result from:\n%S\n", url);
136 }
137
138 ajStrDel(&url);
139 ajStrDel(&restid);
140 ajStrDel(&seqid);
141 ajStrDel(&inseq);
142 }
143
144 ajFileClose(&outf);
145
146 ajSeqallDel(&seqall);
147 ajSeqDel(&seq);
148 ajStrDel(&base);
149
150 ajStrDel(&delkey);
151
152 embExit();
153
154 return 0;
155 }