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comparison GEMBASSY-1.0.3/src/gb1.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 gb1
3 **
4 ** Calculate strand bias of bacterial genome using B1 index
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 gb1 ******************************************************************
35 **
36 ** Calculate strand bias of bacterial genome using B1 index
37 **
38 ******************************************************************************/
39
40 int main(int argc, char *argv[])
41 {
42 embInitPV("gb1", argc, argv, "GEMBASSY", "1.0.3");
43
44 AjPSeqall seqall;
45 AjPSeq seq;
46 AjPStr inseq = NULL;
47
48 AjBool accid = ajFalse;
49 AjPStr restid = NULL;
50 AjPStr seqid = NULL;
51
52 AjPStr base = NULL;
53 AjPStr url = NULL;
54
55 AjPStr method = NULL;
56
57 AjPFile outf = NULL;
58
59 AjPFile tmpfile = NULL;
60 AjPStr tmpname = NULL;
61
62 AjPFilebuff tmp = NULL;
63 AjPStr line = NULL;
64
65 seqall = ajAcdGetSeqall("sequence");
66 method = ajAcdGetSelectSingle("method");
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/B1/method=%S", base, restid, method);
131
132 if(!gFilebuffURLS(url, &tmp))
133 {
134 ajDie("Failed to download result from:\n%S\n", url);
135 }
136
137 ajBuffreadLine(tmp, &line);
138
139 ajStrRemoveSetC(&line, "\n");
140
141 ajFmtPrintF(outf, "Sequence: %S B1: %S\n", seqid, line);
142
143 ajStrDel(&url);
144 ajStrDel(&restid);
145 ajStrDel(&seqid);
146 ajStrDel(&inseq);
147 }
148
149 ajFileClose(&outf);
150
151 ajSeqallDel(&seqall);
152 ajSeqDel(&seq);
153 ajStrDel(&base);
154
155 ajStrDel(&method);
156
157 embExit();
158
159 return 0;
160 }