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

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author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
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1 /******************************************************************************
2 ** @source ggenomicskew
3 **
4 ** Calculates the GC skew in different regions of the given genome
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 ggenomicskew *********************************************************
36 **
37 ** Calculates the GC skew in different regions of the given genome
38 **
39 ******************************************************************************/
40
41 int main(int argc, char *argv[])
42 {
43 embInitPV("ggenomicskew", argc, argv, "GEMBASSY", "1.0.3");
44
45 AjPSeqall seqall;
46 AjPSeq seq;
47 AjPStr inseq = NULL;
48
49 ajint divide = 0;
50 AjBool at = 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 AjBool plot = 0;
63 AjPFile outf = NULL;
64 AjPFilebuff buff = NULL;
65 AjPGraph mult = NULL;
66
67 gPlotParams gpp;
68 AjPStr title = NULL;
69 AjPPStr names = NULL;
70
71 ajint i;
72
73 seqall = ajAcdGetSeqall("sequence");
74 divide = ajAcdGetInt("divide");
75 at = ajAcdGetBoolean("at");
76 accid = ajAcdGetBoolean("accid");
77
78 plot = ajAcdGetToggle("plot");
79 outf = ajAcdGetOutfile("outfile");
80 mult = ajAcdGetGraphxy("graph");
81
82 base = ajStrNewC("rest.g-language.org");
83
84 gAssignUniqueName(&tmpname);
85
86 while (ajSeqallNext(seqall, &seq))
87 {
88 inseq = NULL;
89
90 if(!accid)
91 {
92 if(gFormatGenbank(seq, &inseq))
93 {
94 gAssignUniqueName(&tmpname);
95
96 tmpfile = ajFileNewOutNameS(tmpname);
97
98 if(!tmpfile)
99 {
100 ajFmtError("Output file (%S) open error\n", tmpname);
101 embExitBad();
102 }
103
104 ajFmtPrintF(tmpfile, "%S", inseq);
105 ajFileClose(&tmpfile);
106 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
107 gFilePostSS(url, tmpname, &restid);
108 ajStrDel(&url);
109 ajSysFileUnlinkS(tmpname);
110 }
111 else
112 {
113 ajFmtError("Sequence does not have features\n"
114 "Proceeding with sequence accession ID\n");
115 accid = ajTrue;
116 }
117 }
118
119 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
120
121 if(ajStrGetLen(seqid) == 0)
122 {
123 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
124 }
125
126 if(ajStrGetLen(seqid) == 0)
127 {
128 ajWarn("No valid header information\n");
129 }
130
131 if(accid)
132 {
133 ajStrAssignS(&restid, seqid);
134 if(ajStrGetLen(seqid) == 0)
135 {
136 ajDie("Cannot proceed without header with -accid\n");
137 }
138
139 if(!gValID(seqid))
140 {
141 ajDie("Invalid accession ID:%S, exiting\n", seqid);
142 }
143 }
144
145 url = ajStrNew();
146
147 ajFmtPrintS(&url, "http://%S/%S/genomicskew/divide=%d/at=%d/"
148 "output=f/tag=gene", base, restid, divide, at);
149 if(plot)
150 {
151 if((names = (AjPPStr)malloc(sizeof(AjPStr) * 5)) == NULL) {
152 ajDie("Error in memory allocation, exiting\n");
153 }
154
155 names[0] = NULL;
156 names[1] = ajStrNewC("whole genome");
157 names[2] = ajStrNewC("coding region");
158 names[3] = ajStrNewC("intergenic region");
159 names[4] = ajStrNewC("codon third position");
160
161 ajStrAppendC(&title, argv[0]);
162 ajStrAppendC(&title, " of ");
163 ajStrAppendS(&title, seqid);
164
165 gpp.title = ajStrNewS(title);
166 gpp.xlab = ajStrNewC("location");
167 gpp.ylab = ajStrNewC("GC skew");
168 gpp.names = names;
169
170 if(!gFilebuffURLS(url, &buff))
171 {
172 ajDie("File downloading error from:\n%S\n", url);
173 }
174
175 if(!gPlotFilebuff(buff, mult, &gpp))
176 {
177 ajDie("Error in plotting\n");
178 }
179
180 i = 0;
181 while(names[i])
182 {
183 AJFREE(names[i]);
184 ++i;
185 }
186
187 AJFREE(names);
188
189 ajStrDel(&title);
190 ajStrDel(&(gpp.title));
191 ajStrDel(&(gpp.xlab));
192 ajStrDel(&(gpp.ylab));
193 ajFilebuffDel(&buff);
194 }
195 else
196 {
197 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
198 if(!gFileOutURLS(url, &outf))
199 {
200 ajDie("File downloading error from:\n%S\n", url);
201 }
202 }
203
204 ajStrDel(&url);
205 ajStrDel(&restid);
206 ajStrDel(&seqid);
207 ajStrDel(&inseq);
208 }
209
210 ajFileClose(&outf);
211
212 ajSeqallDel(&seqall);
213 ajSeqDel(&seq);
214 ajStrDel(&base);
215
216 embExit();
217
218 return 0;
219 }