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