1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
|
static char const rcsid[] = "$Id: fastacmd.c,v 6.36 2005/06/22 13:55:22 coulouri Exp $";
/* $Id: fastacmd.c,v 6.36 2005/06/22 13:55:22 coulouri Exp $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* File Name: $RCSfile: fastacmd.c,v $
*
* Author: Sergei Shavirin
*
* Initial Version Creation Date: 05/20/1997
*
* $Revision: 6.36 $
*
* File Description:
* FASTA retrievel system using ISAM indexes
*
* $Log: fastacmd.c,v $
* Revision 6.36 2005/06/22 13:55:22 coulouri
* add support for dumping accessions
*
* Revision 6.35 2005/05/05 15:54:06 dondosha
* Enhanced comment for the -s option and fixed typo in -i option description
*
* Revision 6.34 2004/12/04 03:39:48 camacho
* Set range of data on -D option
*
* Revision 6.33 2004/12/03 04:58:06 camacho
* Fix name conflict in enumeration for fastacmd dump types
*
* Revision 6.32 2004/12/02 20:37:40 camacho
* + fastacmd feature to dump list of gis
*
* Revision 6.31 2004/06/30 19:52:00 camacho
* Added #include <blfmtutl.h>
*
* Revision 6.30 2004/05/13 20:54:45 coulouri
* spell 'loci' correctly
*
* Revision 6.29 2003/05/30 17:31:09 coulouri
* add rcsid
*
* Revision 6.28 2003/04/15 19:09:41 camacho
* Added option to retrieve sequences by PIG
*
* Revision 6.27 2002/11/21 21:35:54 camacho
* Make sure the proper exit code is returned
*
* Revision 6.26 2002/08/12 12:40:55 camacho
* Fix for unresolved symbol in Win32 build
*
* Revision 6.25 2002/08/09 19:41:25 camacho
* 1) Added blast version number to command-line options
* 2) Added explanations for some default parameters
*
* Revision 6.24 2002/07/30 21:02:17 camacho
* Added explanation for -T option
*
* Revision 6.23 2002/07/30 15:30:47 camacho
* 1. Added explanation for -L option
* 2. Moved function to parse SeqLocs to readdb.c
*
* Revision 6.22 2002/07/18 22:17:49 madden
* Revert last change
*
* Revision 6.21 2002/07/18 18:49:43 madden
* Set SeqLoc to NULL always
*
* Revision 6.20 2002/07/14 21:02:08 camacho
* Added extra features to fastacmd
*
* Revision 6.19 2002/05/02 21:59:31 camacho
* Clarified database parameter default
*
* Revision 6.18 2001/12/18 13:01:52 camacho
* Added new flag -D to dump blast database in FASTA format
*
* Revision 6.17 2001/12/10 19:17:32 camacho
* Added option to allow fastacmd to use Ctrl-As as defline separators.
*
* Revision 6.16 2001/10/19 19:46:26 camacho
* Added new feature to dump FASTA files from blast databases, added support for the new database format
*
* Revision 6.15 2000/10/16 20:47:35 madden
* Add -o option to write output to file
*
* Revision 6.14 2000/06/28 16:56:52 madden
* Call Fastacmd_Search_ex, Boolean for target gi only
*
* Revision 6.13 2000/03/08 15:26:03 madden
* Add return statement to Main fct, purify nit
*
* Revision 6.12 2000/01/12 21:05:00 egorov
* Use Fastacmd API
*
* Revision 6.11 1999/12/21 21:26:22 egorov
* Use new parameter of readdb_gi2seq function
*
* Revision 6.10 1999/12/17 20:48:54 egorov
* Fix 'gcc -Wall' warnings and remove old stuff.
*
* Revision 6.9 1999/09/28 19:02:47 egorov
* In the new version of the 'fastacmd' there is not need to
* specify database name if search a GI.
*
* Revision 6.8 1999/02/23 17:17:32 madden
* Remove unused static _accession functions
*
* Revision 6.7 1998/02/11 18:06:43 madden
* Fix for reading IDs in from a file
*
* Revision 6.6 1998/02/06 18:26:35 madden
* Removed stripping of white spaces
*
* Revision 6.5 1998/01/29 19:47:02 madden
* Changed second call from BioseqRawToFasta to BioseqRawToFastaExtra
*
* Revision 6.4 1998/01/27 20:27:03 madden
* Added option to specify sequence line length
*
* Revision 6.3 1998/01/23 21:56:16 madden
* Error messages sent to stderr
*
* Revision 6.2 1998/01/16 22:04:20 madden
* Call to readdb_new_ex, fixed FUM
*
* Revision 6.1 1997/11/07 16:19:15 shavirin
* Added possibility to retrieve redundant accessions
*
* Revision 6.0 1997/08/25 18:19:56 madden
* Revision changed to 6.0
*
* Revision 5.2 1997/05/20 21:00:45 shavirin
* Remove spurious error message in accession/locus retrieval
*
* Revision 5.1 1997/05/20 15:47:30 shavirin
* Initial revision
*
*
* ==========================================================================
*/
#include <ncbi.h>
#include <objseq.h>
#include <objsset.h>
#include <sequtil.h>
#include <seqport.h>
#include <tofasta.h>
#include <readdb.h>
#include <blast.h>
#include <blfmtutl.h>
static Args myargs [] = {
{ "Database", /* 0 */
"nr", NULL, NULL, TRUE, 'd', ARG_STRING, 0.0, 0, NULL},
{ "Type of file\n" /* 1 */
" G - guess mode (look for protein, then nucleotide)\n"
" T - protein \n"
" F - nucleotide",
"G", NULL,NULL,TRUE,'p',ARG_STRING,0.0,0,NULL},
{ "Comma-delimited search string(s).\n"
" GIs, accessions, loci, or fullSeq-id strings may be used,\n"
" e.g. 555, AC147927, 'gnl|dbname|tag'", /* 2 */
NULL, NULL, NULL, TRUE, 's', ARG_STRING, 0.0, 0, NULL},
{ "Input file with GIs/accessions/loci for batch\n"
" retrieval", /* 3 */
NULL, NULL, NULL, TRUE, 'i', ARG_STRING, 0.0, 0, NULL},
{ "Retrieve duplicate accessions", /* 4 */
"F", NULL, NULL, TRUE, 'a', ARG_BOOLEAN, 0.0, 0, NULL},
{ "Line length for sequence", /* 5 */
"80", NULL, NULL, TRUE, 'l', ARG_INT, 0.0, 0, NULL},
{ "Definition line should contain target gi only", /* 6 */
"F", NULL, NULL, TRUE, 't', ARG_BOOLEAN, 0.0, 0, NULL},
{ "Output file", /* 7 */
"stdout", NULL, NULL, TRUE, 'o', ARG_FILE_OUT, 0.0, 0, NULL},
{ "Use Ctrl-A's as non-redundant defline separator", /* 8 */
"F", NULL, NULL, TRUE, 'c', ARG_BOOLEAN, 0.0, 0, NULL},
{ "Dump the entire database as (default is not to dump anything):\n"
" 1 FASTA\n"
" 2 Gi list\n"
" 3 Accession.version list\n", /* 9 */
"0", "0", "3", TRUE, 'D', ARG_INT, 0.0, 0, NULL},
{ "Range of sequence to extract (Format: start,stop)\n"
" 0 in 'start' refers to the beginning of the sequence\n"
" 0 in 'stop' refers to the end of the sequence",
"0,0", NULL, NULL, TRUE, 'L', ARG_STRING, 0.0, 0, NULL}, /* 10 */
{ "Strand on subsequence (nucleotide only): 1 is top, 2 is bottom",
"1", NULL, NULL, FALSE, 'S', ARG_INT, 0.0, 0, NULL}, /* 11 */
{ "Print taxonomic information for requested sequence(s)",
"F", NULL, NULL, FALSE, 'T', ARG_BOOLEAN, 0.0, 0, NULL}, /* 12 */
{ "Print database information only (overrides all other options)",
"F", NULL, NULL, FALSE, 'I', ARG_BOOLEAN, 0.0, 0, NULL}, /* 13 */
{ "Retrieve sequences with this PIG",
NULL, NULL, NULL, TRUE, 'P', ARG_INT, 0.0, 0, NULL}, /* 14 */
};
Int2 Main (void)
{
CharPtr database, searchstr, batchfile;
Int4 linelen, pig;
Boolean dupl, target, use_ctrlAs, taxonomy_info, dbinfo_only;
EBlastDbDumpType dump_db = eNoDump;
Uint1 is_prot;
FILE *outfp = NULL;
CharPtr seqlocstr;
Uint1 strand;
Char buf[256] = { '\0' };
Int2 rv;
StringCpy(buf, "fastacmd ");
StringNCat(buf, BlastGetVersionNumber(), sizeof(buf)-StringLen(buf));
if (! GetArgs (buf, DIM(myargs), myargs)) {
return (1);
}
if( !ErrSetLogfile ("stderr", ELOG_APPEND) ) {
exit(1);
}
database = myargs[0].strvalue;
if (!StringICmp(myargs[1].strvalue, "T"))
is_prot = READDB_DB_IS_PROT;
else if (!StringICmp(myargs[1].strvalue, "F"))
is_prot = READDB_DB_IS_NUC;
else
is_prot = READDB_DB_UNKNOWN;
searchstr = myargs[2].strvalue;
batchfile = myargs[3].strvalue;
dupl = myargs[4].intvalue;
linelen = myargs[5].intvalue;
target = myargs[6].intvalue;
use_ctrlAs = myargs[8].intvalue;
dump_db = myargs[9].intvalue;
seqlocstr = myargs[10].strvalue;
strand = myargs[11].intvalue;
taxonomy_info = myargs[12].intvalue;
dbinfo_only = myargs[13].intvalue;
pig = myargs[14].intvalue == 0 ? PIG_NONE : myargs[14].intvalue;
if ((outfp = FileOpen(myargs[7].strvalue, "w")) == NULL) {
ErrPostEx(SEV_ERROR, 0, 0,"Could not open %s", myargs[7].strvalue);
return 1;
}
rv = Fastacmd_Search_ex (searchstr, database, is_prot, batchfile, dupl,
linelen, outfp, target, use_ctrlAs, dump_db, seqlocstr, strand,
taxonomy_info, dbinfo_only, pig);
FileClose(outfp);
return rv;
}
|