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<HTML>
<HEAD>
<TITLE>
EMBOSS: dbxflat
</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">
dbxflat
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Database b+tree indexing for flat 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>dbxflat</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 embl [
type: N
dbalias: embl (see below)
format: embl
method: emboss
directory: /data/embl
file: *.dat
indexdirectory: /data/embl/indexes
]
</pre>
The index file 'basename' given to <b>dbxflat</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>dbxflat</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>dbxflat</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 dbxflat</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>dbxflat </b>
Database b+tree indexing for flat file databases
Basename for index files: <b>embl</b>
Resource name: <b>embl</b>
EMBL : EMBL
SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
GB : Genbank, DDBJ
REFSEQ : Refseq
Entry format [SWISS]: <b>embl</b>
Wildcard database filename [*.dat]: <b>rod.dat</b>
Database directory [.]: <b>embl</b>
id : ID
acc : Accession number
sv : Sequence Version and GI
des : Description
key : Keywords
org : Taxonomy
Index fields [id,acc]: <b></b>
Processing file /homes/user/test/embl/rod.dat
</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>dbxflat</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>dbxflat</b> is
allowed to cache.
<H2>
Resources
</H2>
<b>dbxflat</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 [SWISS] Entry format (Values: EMBL (EMBL);
SWISS (Swiss-Prot, SpTrEMBL, TrEMBLnew); GB
(Genbank, DDBJ); REFSEQ (Refseq))
-filenames string [*.dat] Wildcard database filename (Any
string is accepted)
-directory directory [.] Database directory
-fields menu [id,acc] Index fields (Values: id (ID); acc
(Accession number); sv (Sequence Version and
GI); des (Description); key (Keywords); org
(Taxonomy))
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-release string [0.0] Release number (Any string up to 9
characters)
-date string [00/00/00] Index date (Date string dd/mm/yy)
-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>Entry format</td>
<td><table><tr><td>EMBL</td> <td><i>(EMBL)</i></td></tr><tr><td>SWISS</td> <td><i>(Swiss-Prot, SpTrEMBL, TrEMBLnew)</i></td></tr><tr><td>GB</td> <td><i>(Genbank, DDBJ)</i></td></tr><tr><td>REFSEQ</td> <td><i>(Refseq)</i></td></tr></table></td>
<td>SWISS</td>
</tr>
<tr>
<td>-filenames</td>
<td>Wildcard database filename</td>
<td>Any string is accepted</td>
<td>*.dat</td>
</tr>
<tr>
<td>-directory</td>
<td>Database directory</td>
<td>Directory</td>
<td>.</td>
</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><tr><td>key</td> <td><i>(Keywords)</i></td></tr><tr><td>org</td> <td><i>(Taxonomy)</i></td></tr></table></td>
<td>id,acc</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>-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>
<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>dbxflat</b> reads any normal sequence USAs.
<p>
<H2>
Output file format
</H2>
<b>dbxflat</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: embl.ent</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
# Number of files: 1
# Release: 0.0
# Date: 00/00/00
Single filename database
rod.dat
</pre>
</td></tr></table><p>
<p><h3>File: embl.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 8
Kwlimit 15
</pre>
</td></tr></table><p>
<p><h3>File: embl.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: embl.xac</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: embl.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="dbxfasta.html">dbxfasta</a></td>
<td>Database b+tree indexing for fasta 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>