-
Notifications
You must be signed in to change notification settings - Fork 0
/
dbxfasta.html
657 lines (449 loc) · 12.8 KB
/
dbxfasta.html
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
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
<HTML>
<HEAD>
<TITLE>
EMBOSS: dbxfasta
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
dbxfasta
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Database b+tree indexing for fasta file databases
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->
<H2>
Description
</H2>
<!--
This is the main part of the document.
This is what the user looks at to find out if this program will do what he wants.
Long description.
Why it is useful.
When it should/shouldn't be used.
-->
<b>dbxfasta</b> indexes a flat file database of one or more files, and builds
EMBOSS B+tree format index files. These indexes allow access of flat
files larger than 2Gb.
<p>
Having created the EMBOSS indexes for this file, a database can then be
defined in the file <b>emboss.defaults</b> as something like:
<pre>
DB emrod [
type: N
dbalias: emrod (see below)
format: fasta
method: emboss
directory: /data/embl/fasta
file: emrod.fasta
indexdirectory: /data/embl/fasta/indexes
]
</pre>
The index file 'basename' given to <b>dbxfasta</b> must match the DB name
in the definition. If not, then a 'dbalias' line must be given which
specifies the basename of the indexes.
<h3>Fields Indexed</H3>
By default, <b>dbxfasta</b> will index the ID name and the accession
number (if present).
<br>
If they are present in your database, you may also specify that
<b>dbxfasta</b> should index the Sequence Version and GI, the words
in the description, the keywords and the organism words using the
'-fields' qualifier with the appropriate values.
<H2>
Usage
</H2>
<!--
Example usage, as run from the command-line.
Many examples illustrating different behaviours is good.
-->
<b>Here is a sample session with dbxfasta</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>dbxfasta </b>
Database b+tree indexing for fasta file databases
Basename for index files: <b>emrod</b>
Resource name: <b>embl</b>
simple : >ID
idacc : >ID ACC or >ID (ACC)
gcgid : >db:ID
gcgidacc : >db:ID ACC
dbid : >db ID
ncbi : | formats
ID line format [idacc]: <b>idacc</b>
Database directory [.]: <b>data</b>
Wildcard database filename [*.dat]: <b>emrod</b>
Release number [0.0]: <b></b>
Index date [00/00/00]: <b></b>
Processing file /homes/user/test/data/emrod
</pre></td></tr></table><p>
<p>
<a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Global Parameters
</H2>
<b>dbxfasta</b> requires that two global parameters be defined in
the file <b>emboss.defaults</b>. These are:
<pre>
SET PAGESIZE 2048
SET CACHESIZE 200
</pre>
The above values are recommended for most systems. The PAGESIZE is
a multiple of the size of disc pages the operating system buffers.
The CACHESIZE is the number of disc pages <b>dbxfasta</b> is
allowed to cache.
<H2>
Resources
</H2>
<b>dbxfasta</b> will ask you for the name of a resource definition
in the file <b>emboss.defaults</b>. This will be something like:
<pre>
RES embl [
type: Index
idlen: 15
acclen: 15
svlen: 20
keylen: 25
deslen: 25
orglen: 25
]
</pre>
The length definitions are the maximum lengths of 'words' in the
field being indexed. Longer words will be truncated to the
value set.
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Standard (Mandatory) qualifiers:
[-dbname] string Basename for index files (Any string from 2
to 19 characters, matching regular
expression /[A-z][A-z0-9_]+/)
[-dbresource] string Resource name (Any string from 2 to 19
characters, matching regular expression
/[A-z][A-z0-9_]+/)
-idformat menu [idacc] ID line format (Values: simple
(>ID); idacc (>ID ACC or >ID (ACC)); gcgid
(>db:ID); gcgidacc (>db:ID ACC); dbid (>db
ID); ncbi (| formats))
-directory directory [.] Database directory
-filenames string [*.dat] Wildcard database filename (Any
string is accepted)
-release string [0.0] Release number (Any string up to 9
characters)
-date string [00/00/00] Index date (Date string dd/mm/yy)
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-fields menu [id,acc] Index fields (Values: id (ID); acc
(Accession number); sv (Sequence Version and
GI); des (Description))
-exclude string Wildcard filename(s) to exclude (Any string
is accepted)
-indexoutdir outdir [.] Index file output directory
Associated qualifiers: (none)
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-dbname]<br>(Parameter 1)</td>
<td>Basename for index files</td>
<td>Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-dbresource]<br>(Parameter 2)</td>
<td>Resource name</td>
<td>Any string from 2 to 19 characters, matching regular expression /[A-z][A-z0-9_]+/</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>-idformat</td>
<td>ID line format</td>
<td><table><tr><td>simple</td> <td><i>(>ID)</i></td></tr><tr><td>idacc</td> <td><i>(>ID ACC or >ID (ACC))</i></td></tr><tr><td>gcgid</td> <td><i>(>db:ID)</i></td></tr><tr><td>gcgidacc</td> <td><i>(>db:ID ACC)</i></td></tr><tr><td>dbid</td> <td><i>(>db ID)</i></td></tr><tr><td>ncbi</td> <td><i>(| formats)</i></td></tr></table></td>
<td>idacc</td>
</tr>
<tr>
<td>-directory</td>
<td>Database directory</td>
<td>Directory</td>
<td>.</td>
</tr>
<tr>
<td>-filenames</td>
<td>Wildcard database filename</td>
<td>Any string is accepted</td>
<td>*.dat</td>
</tr>
<tr>
<td>-release</td>
<td>Release number</td>
<td>Any string up to 9 characters</td>
<td>0.0</td>
</tr>
<tr>
<td>-date</td>
<td>Index date</td>
<td>Date string dd/mm/yy</td>
<td>00/00/00</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-fields</td>
<td>Index fields</td>
<td><table><tr><td>id</td> <td><i>(ID)</i></td></tr><tr><td>acc</td> <td><i>(Accession number)</i></td></tr><tr><td>sv</td> <td><i>(Sequence Version and GI)</i></td></tr><tr><td>des</td> <td><i>(Description)</i></td></tr></table></td>
<td>id,acc</td>
</tr>
<tr>
<td>-exclude</td>
<td>Wildcard filename(s) to exclude</td>
<td>Any string is accepted</td>
<td><i>An empty string is accepted</i></td>
</tr>
<tr>
<td>-indexoutdir</td>
<td>Index file output directory</td>
<td>Output directory</td>
<td>.</td>
</tr>
</table>
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->
<H2>
Input file format
</H2>
<!--
This includes example input file formats.
This should be a detailed description and example - assume
someone will want to parse this file and will want to know what
happens in unusual cases - null input, etc.
-->
<b>dbxfasta</b> reads any normal sequence USAs.
<p>
<H2>
Output file format
</H2>
<b>dbxfasta</b> creates one summary file for the database and two files
for each field indexed.
<p>
<ul>
<li>dbalias.ent is the master file containing the names of the files
that have been indexed. It is an ASCII file. This file also contains
the database release and date information.
<li>dbalias.xid is the B+tree index file for the ID names. It is a binary
file.
<li>dbalias.pxid is an ASCII file containing information regarding the
structure of the ID name index.
</ul>
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: emrod.ent</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
# Number of files: 1
# Release: 0.0
# Date: 00/00/00
Single filename database
emrod
</pre>
</td></tr></table><p>
<p><h3>File: emrod.pxac</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Order 71
Fill 47
Pagesize 2048
Level 0
Cachesize 200
Order2 82
Fill2 99
Count 5
Kwlimit 15
</pre>
</td></tr></table><p>
<p><h3>File: emrod.pxid</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Order 71
Fill 47
Pagesize 2048
Level 0
Cachesize 200
Order2 82
Fill2 99
Count 5
Kwlimit 15
</pre>
</td></tr></table><p>
<p><h3>File: emrod.xac</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: emrod.xid</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
<!--
Restrictions.
Interesting behaviour.
Useful things you can do with this program.
-->
The indexing system has been designed to allow on-the-fly updating
of indexes. This feature is, however, not implemented in the current
version. It will be made available in future releases.
<H2>
References
</H2>
<!--
Bibliography for methods used.
<ol>
<li>
</ol>
-->
None.
<H2>
Warnings
</H2>
<!--
Potentially stupid things the program will let you do.
-->
None.
<H2>
Diagnostic Error Messages
</H2>
<!--
Error messages specific to this program, eg:
"FATAL xxx" - means you have not set up the xxx data using program <b>prog</b>.<p>
-->
None.
<H2>
Exit status
</H2>
<!--
Description of the exit status for various error conditions
-->
It always exits with status 0.
<H2>
Known bugs
</H2>
<!--
Bugs noted but not yet fixed.
-->
None.
<!--
<H2>
See also
</H2>
-->
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="dbiblast.html">dbiblast</a></td>
<td>Index a BLAST database</td>
</tr>
<tr>
<td><a href="dbifasta.html">dbifasta</a></td>
<td>Database indexing for fasta file databases</td>
</tr>
<tr>
<td><a href="dbiflat.html">dbiflat</a></td>
<td>Index a flat file database</td>
</tr>
<tr>
<td><a href="dbigcg.html">dbigcg</a></td>
<td>Index a GCG formatted database</td>
</tr>
<tr>
<td><a href="dbxflat.html">dbxflat</a></td>
<td>Database b+tree indexing for flat file databases</td>
</tr>
<tr>
<td><a href="dbxgcg.html">dbxgcg</a></td>
<td>Database b+tree indexing for GCG formatted databases</td>
</tr>
</table>
<!--
Add any comments about other associated programs (to prepare
data files?) that seealso doesn't find.
-->
<H2>
Author(s)
</H2>
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
<!--
Date written and what changes have been made go in this file.
-->
<H2>
Target users
</H2>
<!--
For general users, use this text
-->
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
<!--
User/developer/other comments go in this file.
-->
None
</BODY>
</HTML>