Mercurial > repos > ktnyt > gembassy
comparison GEMBASSY-1.0.3/src/gdeltagcskew.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 /****************************************************************************** | |
2 ** @source gdeltagcskew | |
3 ** | |
4 ** Calculates strand bias of bacterial genome using delta GC skew 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 gdeltagcskew ******************************************************** | |
35 ** | |
36 ** Calculates strand bias of bacterial genome using delta GC skew index | |
37 ** | |
38 ******************************************************************************/ | |
39 | |
40 int main(int argc, char *argv[]) | |
41 { | |
42 embInitPV("gdeltagcskew", argc, argv, "GEMBASSY", "1.0.3"); | |
43 | |
44 AjPSeqall seqall; | |
45 AjPSeq seq; | |
46 AjPStr inseq = NULL; | |
47 | |
48 AjBool at = 0; | |
49 AjBool purine = 0; | |
50 AjBool keto = 0; | |
51 AjPStr method = 0; | |
52 | |
53 AjBool accid = ajFalse; | |
54 AjPStr restid = NULL; | |
55 AjPStr seqid = NULL; | |
56 | |
57 AjPStr base = NULL; | |
58 AjPStr url = NULL; | |
59 | |
60 AjPFile tmpfile = NULL; | |
61 AjPStr tmpname = NULL; | |
62 AjPFilebuff tmp = NULL; | |
63 | |
64 AjPStr line = NULL; | |
65 | |
66 AjPFile outf = NULL; | |
67 | |
68 seqall = ajAcdGetSeqall("sequence"); | |
69 at = ajAcdGetBoolean("at"); | |
70 purine = ajAcdGetBoolean("purine"); | |
71 keto = ajAcdGetBoolean("keto"); | |
72 method = ajAcdGetSelectSingle("method"); | |
73 accid = ajAcdGetBoolean("accid"); | |
74 outf = ajAcdGetOutfile("outfile"); | |
75 | |
76 base = ajStrNewC("rest.g-language.org"); | |
77 | |
78 gAssignUniqueName(&tmpname); | |
79 | |
80 while(ajSeqallNext(seqall, &seq)) | |
81 { | |
82 inseq = NULL; | |
83 | |
84 if(!accid) | |
85 { | |
86 if(gFormatGenbank(seq, &inseq)) | |
87 { | |
88 tmpfile = ajFileNewOutNameS(tmpname); | |
89 if(!tmpfile) | |
90 { | |
91 ajDie("Output file (%S) open error\n", tmpname); | |
92 } | |
93 ajFmtPrintF(tmpfile, "%S", inseq); | |
94 ajFileClose(&tmpfile); | |
95 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base); | |
96 gFilePostSS(url, tmpname, &restid); | |
97 ajStrDel(&url); | |
98 ajSysFileUnlinkS(tmpname); | |
99 } | |
100 else | |
101 { | |
102 ajWarn("Sequence does not have features\n" | |
103 "Proceeding with sequence accession ID\n"); | |
104 accid = ajTrue; | |
105 } | |
106 } | |
107 | |
108 ajStrAssignS(&seqid, ajSeqGetAccS(seq)); | |
109 | |
110 if(ajStrGetLen(seqid) == 0) | |
111 { | |
112 ajStrAssignS(&seqid, ajSeqGetNameS(seq)); | |
113 } | |
114 | |
115 if(ajStrGetLen(seqid) == 0) | |
116 { | |
117 ajWarn("No valid header information\n"); | |
118 } | |
119 | |
120 if(accid) | |
121 { | |
122 ajStrAssignS(&restid, seqid); | |
123 if(ajStrGetLen(seqid) == 0) | |
124 { | |
125 ajDie("Cannot proceed without header with -accid\n"); | |
126 } | |
127 | |
128 if(!gValID(seqid)) | |
129 { | |
130 ajDie("Invalid accession ID:%S, exiting\n", seqid); | |
131 } | |
132 } | |
133 | |
134 url = ajStrNew(); | |
135 | |
136 ajFmtPrintS(&url, "http://%S/%S/delta_gcskew/", base, restid); | |
137 | |
138 if(!gFilebuffURLS(url, &tmp)) | |
139 { | |
140 ajDie("Failed to download result from:\n%S\n", url); | |
141 } | |
142 | |
143 ajBuffreadLine(tmp, &line); | |
144 | |
145 ajStrRemoveSetC(&line, "\n"); | |
146 | |
147 ajFmtPrintF(outf, "Sequence: %S DELTA-GCskew %S\n", seqid, line); | |
148 | |
149 ajStrDel(&url); | |
150 ajStrDel(&restid); | |
151 ajStrDel(&seqid); | |
152 ajStrDel(&inseq); | |
153 } | |
154 | |
155 ajFileClose(&outf); | |
156 | |
157 ajSeqallDel(&seqall); | |
158 ajSeqDel(&seq); | |
159 ajStrDel(&base); | |
160 | |
161 embExit(); | |
162 | |
163 return 0; | |
164 } |