Mercurial > repos > ktnyt > gembassy
comparison GEMBASSY-1.0.3/src/gp2.c @ 0:8300eb051bea draft
Initial upload
author | ktnyt |
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date | Fri, 26 Jun 2015 05:19:29 -0400 |
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-1:000000000000 | 0:8300eb051bea |
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1 /****************************************************************************** | |
2 ** @source gp2 | |
3 ** | |
4 ** | |
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 gp2 ****************************************************************** | |
35 ** | |
36 ** Predict highly expressed gene | |
37 ** | |
38 ******************************************************************************/ | |
39 | |
40 int main(int argc, char *argv[]) | |
41 { | |
42 embInitPV("gp2", 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 AjPFile tmpfile = NULL; | |
56 AjPStr tmpname = NULL; | |
57 | |
58 AjPFile outf = NULL; | |
59 | |
60 seqall = ajAcdGetSeqall("sequence"); | |
61 accid = ajAcdGetBoolean("accid"); | |
62 outf = ajAcdGetOutfile("outfile"); | |
63 | |
64 base = ajStrNewC("rest.g-language.org"); | |
65 | |
66 gAssignUniqueName(&tmpname); | |
67 | |
68 while(ajSeqallNext(seqall, &seq)) | |
69 { | |
70 inseq = NULL; | |
71 | |
72 if(!accid) | |
73 { | |
74 if(gFormatGenbank(seq, &inseq)) | |
75 { | |
76 tmpfile = ajFileNewOutNameS(tmpname); | |
77 if(!tmpfile) | |
78 { | |
79 ajDie("Output file (%S) open error\n", tmpname); | |
80 } | |
81 ajFmtPrintF(tmpfile, "%S", inseq); | |
82 ajFileClose(&tmpfile); | |
83 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base); | |
84 gFilePostSS(url, tmpname, &restid); | |
85 ajStrDel(&url); | |
86 ajSysFileUnlinkS(tmpname); | |
87 } | |
88 else | |
89 { | |
90 ajWarn("Sequence does not have features\n" | |
91 "Proceeding with sequence accession ID\n"); | |
92 accid = ajTrue; | |
93 } | |
94 } | |
95 | |
96 ajStrAssignS(&seqid, ajSeqGetAccS(seq)); | |
97 | |
98 if(ajStrGetLen(seqid) == 0) | |
99 { | |
100 ajStrAssignS(&seqid, ajSeqGetNameS(seq)); | |
101 } | |
102 | |
103 if(ajStrGetLen(seqid) == 0) | |
104 { | |
105 ajWarn("No valid header information\n"); | |
106 } | |
107 | |
108 if(accid) | |
109 { | |
110 ajStrAssignS(&restid, seqid); | |
111 if(ajStrGetLen(seqid) == 0) | |
112 { | |
113 ajDie("Cannot proceed without header with -accid\n"); | |
114 } | |
115 | |
116 if(!gValID(seqid)) | |
117 { | |
118 ajDie("Invalid accession ID:%S, exiting\n", seqid); | |
119 } | |
120 } | |
121 | |
122 url = ajStrNew(); | |
123 | |
124 ajFmtPrintS(&url, "http://%S/%S/P2/output=f/tag=gene", base, restid); | |
125 | |
126 ajFmtPrintF(outf, "Sequence: %S\n", seqid); | |
127 if(!gFileOutURLS(url, &outf)) | |
128 { | |
129 ajDie("Failed to download result from:\n%S\n", url); | |
130 } | |
131 | |
132 ajStrDel(&url); | |
133 ajStrDel(&restid); | |
134 ajStrDel(&seqid); | |
135 ajStrDel(&inseq); | |
136 } | |
137 | |
138 ajFileClose(&outf); | |
139 | |
140 ajSeqallDel(&seqall); | |
141 ajSeqDel(&seq); | |
142 ajStrDel(&base); | |
143 | |
144 embExit(); | |
145 | |
146 return 0; | |
147 } |