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comparison GEMBASSY-1.0.3/src/gnucleotideperiodicity.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 gnucleotideperiodicity
3 **
4 ** Checks the periodicity of certain oligonucleotides
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 "../include/glibs.h"
30
31
32
33
34 /* @prog gnucleotideperiodicity ***********************************************
35 **
36 ** Checks the periodicity of certain oligonucleotides
37 **
38 ******************************************************************************/
39
40 int main(int argc, char *argv[])
41 {
42 embInitPV("gnucleotideperiodicity", argc, argv, "GEMBASSY", "1.0.3");
43
44 AjPSeqall seqall;
45 AjPSeq seq;
46 AjPStr inseq = NULL;
47
48 ajint window = 0;
49 AjPStr nucleotide = NULL;
50
51 AjBool accid = ajFalse;
52 AjPStr restid = NULL;
53 AjPStr seqid = NULL;
54
55 AjPStr base = NULL;
56 AjPStr url = NULL;
57
58 AjPFile tmpfile = NULL;
59 AjPStr tmpname = NULL;
60
61 AjBool plot = 0;
62 AjPFile outf = NULL;
63 AjPFilebuff buff = NULL;
64 AjPGraph mult = NULL;
65
66 gPlotParams gpp;
67 AjPStr title = NULL;
68
69 seqall = ajAcdGetSeqall("sequence");
70 window = ajAcdGetInt("window");
71 nucleotide = ajAcdGetString("nucleotide");
72 accid = ajAcdGetBoolean("accid");
73
74 plot = ajAcdGetToggle("plot");
75 outf = ajAcdGetOutfile("outfile");
76 mult = ajAcdGetGraphxy("graph");
77
78 base = ajStrNewC("rest.g-language.org");
79
80 while(ajSeqallNext(seqall, &seq))
81 {
82 inseq = NULL;
83
84 if(!accid)
85 {
86 if(gFormatGenbank(seq, &inseq))
87 {
88 gAssignUniqueName(&tmpname);
89
90 tmpfile = ajFileNewOutNameS(tmpname);
91
92 if(!tmpfile)
93 {
94 ajFmtError("Output file (%S) open error\n", tmpname);
95 embExitBad();
96 }
97
98 ajFmtPrintF(tmpfile, "%S", inseq);
99 ajFileClose(&tmpfile);
100 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
101 gFilePostSS(url, tmpname, &restid);
102 ajStrDel(&url);
103 ajSysFileUnlinkS(tmpname);
104 }
105 else
106 {
107 ajFmtError("Sequence does not have features\n"
108 "Proceeding with sequence accession ID\n");
109 accid = ajTrue;
110 }
111 }
112
113 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
114
115 if(ajStrGetLen(seqid) == 0)
116 {
117 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
118 }
119
120 if(ajStrGetLen(seqid) == 0)
121 {
122 ajWarn("No valid header information\n");
123 }
124
125 if(accid)
126 {
127 ajStrAssignS(&restid, seqid);
128 if(ajStrGetLen(seqid) == 0)
129 {
130 ajDie("Cannot proceed without header with -accid\n");
131 }
132
133 if(!gValID(seqid))
134 {
135 ajDie("Invalid accession ID:%S, exiting\n", seqid);
136 }
137 }
138
139 url = ajStrNew();
140
141 ajFmtPrintS(&url, "http://%S/%S/nucleotide_periodicity/output=f/gmap=0/"
142 "nucleotide=%S/window=%d", base, restid, nucleotide, window);
143
144 if(plot)
145 {
146 title = ajStrNew();
147
148 ajStrAppendC(&title, argv[0]);
149 ajStrAppendC(&title, " of ");
150 ajStrAppendS(&title, seqid);
151
152 gpp.title = ajStrNewS(title);
153 gpp.xlab = ajStrNewC("window");
154 gpp.ylab = ajStrNewC("value");
155
156 if(!gFilebuffURLS(url, &buff))
157 {
158 ajDie("File downloading error from:\n%S\n", url);
159 }
160
161 if(!gPlotFilebuff(buff, mult, &gpp))
162 {
163 ajDie("Error in plotting\n");
164 }
165
166 AJFREE(gpp.title);
167 AJFREE(gpp.xlab);
168 AJFREE(gpp.ylab);
169 ajStrDel(&title);
170 ajFilebuffDel(&buff);
171 }
172 else
173 {
174 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
175 if(!gFileOutURLS(url, &outf))
176 {
177 ajDie("File downloading error from:\n%S\n", url);
178 }
179 }
180
181 ajStrDel(&url);
182 ajStrDel(&restid);
183 ajStrDel(&seqid);
184 ajStrDel(&inseq);
185 }
186
187 ajSeqallDel(&seqall);
188 ajSeqDel(&seq);
189 ajStrDel(&base);
190
191 embExit();
192
193 return 0;
194 }