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