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