annotate GEMBASSY-1.0.3/src/gnucleotideperiodicity.c @ 1:84a17b3fad1f draft

Uploaded
author ktnyt
date Fri, 26 Jun 2015 05:20:29 -0400
parents 8300eb051bea
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
1 /******************************************************************************
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
2 ** @source gnucleotideperiodicity
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
3 **
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
4 ** Checks the periodicity of certain oligonucleotides
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
5 **
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
6 ** @author Copyright (C) 2012 Hidetoshi Itaya
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
7 ** @version 1.0.3
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
8 ** @modified 2012/1/20 Hidetoshi Itaya Created!
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
9 ** @modified 2013/6/16 Revision 1
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
10 ** @modified 2015/2/7 Refactor
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
11 ** @@
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
12 **
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
13 ** This program is free software; you can redistribute it and/or
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
14 ** modify it under the terms of the GNU General Public License
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
15 ** as published by the Free Software Foundation; either version 2
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
16 ** of the License, or (at your option) any later version.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
17 **
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
18 ** This program is distributed in the hope that it will be useful,
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
19 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
20 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
21 ** GNU General Public License for more details.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
22 **
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
23 ** You should have received a copy of the GNU General Public License
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
24 ** along with this program; if not, write to the Free Software
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
25 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
26 ******************************************************************************/
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
27
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
28 #include "emboss.h"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
29 #include "../include/glibs.h"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
30
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
31
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
32
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
33
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
34 /* @prog gnucleotideperiodicity ***********************************************
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
35 **
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
36 ** Checks the periodicity of certain oligonucleotides
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
37 **
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
38 ******************************************************************************/
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
39
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
40 int main(int argc, char *argv[])
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
41 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
42 embInitPV("gnucleotideperiodicity", argc, argv, "GEMBASSY", "1.0.3");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
43
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
44 AjPSeqall seqall;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
45 AjPSeq seq;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
46 AjPStr inseq = NULL;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
47
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
48 ajint window = 0;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
49 AjPStr nucleotide = NULL;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
50
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
51 AjBool accid = ajFalse;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
52 AjPStr restid = NULL;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
53 AjPStr seqid = NULL;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
54
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
55 AjPStr base = NULL;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
56 AjPStr url = NULL;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
57
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
58 AjPFile tmpfile = NULL;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
59 AjPStr tmpname = NULL;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
60
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
61 AjBool plot = 0;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
62 AjPFile outf = NULL;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
63 AjPFilebuff buff = NULL;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
64 AjPGraph mult = NULL;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
65
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
66 gPlotParams gpp;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
67 AjPStr title = NULL;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
68
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
69 seqall = ajAcdGetSeqall("sequence");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
70 window = ajAcdGetInt("window");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
71 nucleotide = ajAcdGetString("nucleotide");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
72 accid = ajAcdGetBoolean("accid");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
73
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
74 plot = ajAcdGetToggle("plot");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
75 outf = ajAcdGetOutfile("outfile");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
76 mult = ajAcdGetGraphxy("graph");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
77
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
78 base = ajStrNewC("rest.g-language.org");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
79
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
80 while(ajSeqallNext(seqall, &seq))
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
81 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
82 inseq = NULL;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
83
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
84 if(!accid)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
85 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
86 if(gFormatGenbank(seq, &inseq))
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
87 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
88 gAssignUniqueName(&tmpname);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
89
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
90 tmpfile = ajFileNewOutNameS(tmpname);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
91
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
92 if(!tmpfile)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
93 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
94 ajFmtError("Output file (%S) open error\n", tmpname);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
95 embExitBad();
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
96 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
97
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
98 ajFmtPrintF(tmpfile, "%S", inseq);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
99 ajFileClose(&tmpfile);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
100 ajFmtPrintS(&url, "http://%S/upload/upl.pl", base);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
101 gFilePostSS(url, tmpname, &restid);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
102 ajStrDel(&url);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
103 ajSysFileUnlinkS(tmpname);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
104 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
105 else
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
106 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
107 ajFmtError("Sequence does not have features\n"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
108 "Proceeding with sequence accession ID\n");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
109 accid = ajTrue;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
110 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
111 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
112
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
113 ajStrAssignS(&seqid, ajSeqGetAccS(seq));
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
114
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
115 if(ajStrGetLen(seqid) == 0)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
116 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
117 ajStrAssignS(&seqid, ajSeqGetNameS(seq));
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
118 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
119
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
120 if(ajStrGetLen(seqid) == 0)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
121 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
122 ajWarn("No valid header information\n");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
123 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
124
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
125 if(accid)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
126 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
127 ajStrAssignS(&restid, seqid);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
128 if(ajStrGetLen(seqid) == 0)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
129 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
130 ajDie("Cannot proceed without header with -accid\n");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
131 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
132
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
133 if(!gValID(seqid))
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
134 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
135 ajDie("Invalid accession ID:%S, exiting\n", seqid);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
136 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
137 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
138
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
139 url = ajStrNew();
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
140
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
141 ajFmtPrintS(&url, "http://%S/%S/nucleotide_periodicity/output=f/gmap=0/"
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
142 "nucleotide=%S/window=%d", base, restid, nucleotide, window);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
143
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
144 if(plot)
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
145 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
146 title = ajStrNew();
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
147
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
148 ajStrAppendC(&title, argv[0]);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
149 ajStrAppendC(&title, " of ");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
150 ajStrAppendS(&title, seqid);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
151
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
152 gpp.title = ajStrNewS(title);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
153 gpp.xlab = ajStrNewC("window");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
154 gpp.ylab = ajStrNewC("value");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
155
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
156 if(!gFilebuffURLS(url, &buff))
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
157 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
158 ajDie("File downloading error from:\n%S\n", url);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
159 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
160
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
161 if(!gPlotFilebuff(buff, mult, &gpp))
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
162 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
163 ajDie("Error in plotting\n");
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
164 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
165
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
166 AJFREE(gpp.title);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
167 AJFREE(gpp.xlab);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
168 AJFREE(gpp.ylab);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
169 ajStrDel(&title);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
170 ajFilebuffDel(&buff);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
171 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
172 else
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
173 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
174 ajFmtPrintF(outf, "Sequence: %S\n", seqid);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
175 if(!gFileOutURLS(url, &outf))
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
176 {
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
177 ajDie("File downloading error from:\n%S\n", url);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
178 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
179 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
180
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
181 ajStrDel(&url);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
182 ajStrDel(&restid);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
183 ajStrDel(&seqid);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
184 ajStrDel(&inseq);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
185 }
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
186
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
187 ajSeqallDel(&seqall);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
188 ajSeqDel(&seq);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
189 ajStrDel(&base);
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
190
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
191 embExit();
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
192
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
193 return 0;
8300eb051bea Initial upload
ktnyt
parents:
diff changeset
194 }