comparison GEMBASSY-1.0.3/src/gseqinfo.c @ 0:8300eb051bea draft

Initial upload
author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
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1 /******************************************************************************
2 ** @source gseqinfo
3 **
4 ** Prints out basic nucleotide sequence statistics
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 RESTify
11 ** @modified 2015/2/7 Refactor
12 ** @@
13 **
14 ** This program is free software; you can redistribute it and/or
15 ** modify it under the terms of the GNU General Public License
16 ** as published by the Free Software Foundation; either version 2
17 ** of the License, or (at your option) any later version.
18 **
19 ** This program is distributed in the hope that it will be useful,
20 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
21 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22 ** GNU General Public License for more details.
23 **
24 ** You should have received a copy of the GNU General Public License
25 ** along with this program; if not, write to the Free Software
26 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
27 ******************************************************************************/
28
29 #include "emboss.h"
30 #include "glibs.h"
31
32
33
34
35 /* @prog gseqinfo *************************************************************
36 **
37 ** Prints out basic nucleotide sequence statistics
38 **
39 ******************************************************************************/
40
41 int main(int argc, char *argv[])
42 {
43 embInitPV("gseqinfo", argc, argv, "GEMBASSY", "1.0.3");
44
45 AjPSeqall seqall;
46 AjPSeq seq;
47 AjPStr inseq = NULL;
48
49 AjPStr ori = NULL;
50 AjPStr ter = NULL;
51
52 AjPStr restid = NULL;
53 AjPStr seqid = NULL;
54
55 AjPStr base = NULL;
56 AjPStr url = NULL;
57
58 AjPStr tmpname = NULL;
59 AjPSeqout tmpout = NULL;
60
61 AjPFile outf = NULL;
62
63 seqall = ajAcdGetSeqall("sequence");
64 outf = ajAcdGetOutfile("outfile");
65
66 base = ajStrNewC("rest.g-language.org");
67
68 gAssignUniqueName(&tmpname);
69 ajStrAppendC(&tmpname, ".fasta");
70
71 while(ajSeqallNext(seqall, &seq))
72 {
73 tmpout = ajSeqoutNew();
74
75 if(!ajSeqoutOpenFilename(tmpout, tmpname))
76 {
77 embExitBad();
78 }
79
80 ajSeqoutSetFormatS(tmpout,ajStrNewC("fasta"));
81 ajSeqoutWriteSeq(tmpout, seq);
82 ajSeqoutClose(tmpout);
83 ajSeqoutDel(&tmpout);
84
85 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
86 gFilePostSS(url, tmpname, &restid);
87 ajStrDel(&url);
88 ajSysFileUnlinkS(tmpname);
89
90 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
91
92 if(ajStrGetLen(seqid) == 0)
93 {
94 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
95 }
96
97 if(ajStrGetLen(seqid) == 0)
98 {
99 ajWarn("No valid header information\n");
100 }
101
102 url = ajStrNew();
103
104 ajFmtPrintS(&url, "http://%S/%S/seqinfo/", base, restid);
105
106 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
107 if(!gFileOutURLS(url, &outf))
108 {
109 ajDie("Failed to download result from:\n%S\n", url);
110 }
111
112 ajStrDel(&url);
113 ajStrDel(&restid);
114 ajStrDel(&seqid);
115 ajStrDel(&inseq);
116 }
117
118 ajFileClose(&outf);
119
120 ajSeqallDel(&seqall);
121 ajSeqDel(&seq);
122 ajStrDel(&base);
123
124 embExit();
125
126 return 0;
127 }