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<HTML>
<HEAD>
<TITLE>
EMBOSS: dbiflat
</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">
dbiflat
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Index a flat file database
<H2>
Description
</H2>
<b>dbiflat</b> indexes a flat file database of one or more files, and builds
EMBL CD-ROM format index files. This format is used by the software on
the EMBL database CD-ROM distribution and by the Staden package in
addition to EMBOSS, and appears to be the most generally used and
publicly available index file format for these databases.
<p>
A <b>flat file database</b> is a database in one of the native formats:
EMBL, Swiss-Prot or GenBank, as distributed by the EBI, NCBI, or DDBJ.
(It is called a 'flat' file to distinguish it from the complex
relational database formats that this data is held in before being
written to files and distributed.)
<p>
Having created the EMBOSS indices for this file, a database can then be
defined in the file <b>emboss.defaults</b> as something like:
<p>
<pre>
DB emrod [
type: N
format: embl
method: emblcd
directory: /data/embl
]
</pre>
<h3>Fields Indexed</H3>
By default, <b>dbiflat</b> will index the ID name and the accession
number.
<br>
If they are present in your database, you may also specify that
<b>dbiflat</b> should index the Sequence Version and GI number, the
Keywords and Taxonomy names and the words in the description by using
the '-fields' qualifier with the appropriate values.
<H2>
Usage
</H2>
<b>Here is a sample session with dbiflat</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>dbiflat </b>
Index a flat file database
Database name: <b>EMBL</b>
EMBL : EMBL
SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
GB : Genbank, DDBJ
REFSEQ : Refseq
Entry format [SWISS]: <b>EMBL</b>
Database directory [.]: <b>embl</b>
Wildcard database filename [*.dat]: <b>rod.dat</b>
Release number [0.0]: <b></b>
Index date [00/00/00]: <b></b>
General log output file [outfile.dbiflat]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Standard (Mandatory) qualifiers:
[-dbname] string Database 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))
-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)
-outfile outfile [*.dbiflat] General log output file
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-fields menu [acc] Index fields (Values: acc (acnum
accession number index); sv (seqvn sequence
version and gi number index); des (des
description index); key (keyword keywords
index); org (taxon taxonomy and organism
index))
-exclude string Wildcard filename(s) to exclude (Any string
is accepted)
-maxindex integer [0] Maximum index length (Integer 0 or more)
-sortoptions string [-T . -k 1,1] Sort options, typically '-T .'
to use current directory for work files and
'-k 1,1' to force GNU sort to use the first
field (Any string is accepted)
-[no]systemsort boolean [Y] Use system sort utility
-[no]cleanup boolean [Y] Clean up temporary files
-indexoutdir outdir [.] Index file output directory
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory string Output directory
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>Database 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>-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>
<td>-outfile</td>
<td>General log output file</td>
<td>Output file</td>
<td><i><*></i>.dbiflat</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>acc</td> <td><i>(acnum accession number index)</i></td></tr><tr><td>sv</td> <td><i>(seqvn sequence version and gi number index)</i></td></tr><tr><td>des</td> <td><i>(des description index)</i></td></tr><tr><td>key</td> <td><i>(keyword keywords index)</i></td></tr><tr><td>org</td> <td><i>(taxon taxonomy and organism index)</i></td></tr></table></td>
<td>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>-maxindex</td>
<td>Maximum index length</td>
<td>Integer 0 or more</td>
<td>0</td>
</tr>
<tr>
<td>-sortoptions</td>
<td>Sort options, typically '-T .' to use current directory for work files and '-k 1,1' to force GNU sort to use the first field</td>
<td>Any string is accepted</td>
<td>-T . -k 1,1</td>
</tr>
<tr>
<td>-[no]systemsort</td>
<td>Use system sort utility</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>
<tr>
<td>-[no]cleanup</td>
<td>Clean up temporary files</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>
<tr>
<td>-indexoutdir</td>
<td>Index file output directory</td>
<td>Output directory</td>
<td>.</td>
</tr>
</table>
<H2>
Input file format
</H2>
'flat' files (native distribution format) of a protein or nucleic
sequence database.
<p>
<H2>
Output file format
</H2>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: division.lkp</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: entrynam.idx</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: acnum.hit</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: acnum.trg</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: outfile.dbiflat</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: dbiflat
# Rundate: Sun 15 Jul 2007 12:00:00
# Dbname: EMBL
# Release: 0.0
# Date: 15/07/07
# CurrentDirectory: /homes/user/test/qa/dbiflat-ex-keep/
# IndexDirectory: ./
# IndexDirectoryPath: /homes/user/test/qa/dbiflat-ex-keep/
# Maxindex: 0
# Fields: 2
# Field 1: id
# Field 2: acc
# Directory: /homes/user/test/embl/
# DirectoryPath: /homes/user/test/embl/
# Filenames: rod.dat
# Exclude:
# Files: 1
# File 1: /homes/user/test/embl/rod.dat
########################################
# Commandline: dbiflat
# -dbname EMBL
# -idformat EMBL
# -directory ../../embl
# -filenames rod.dat
########################################
filename: 'rod.dat'
id: 6
acc: 9
Index acc: maxlen 6 items 7
Total 1 files 6 entries (0 duplicates)
</pre>
</td></tr></table><p>
<p>
<b>dbiflat</b> creates four index files. All are binary but with a
simple format.
<ul>
<li>division.lkp is the master index file, and has a 300 byte header
containing the database name and date plus information on the record
size. This header is followed by one record for each database file,
giving the full file name for the data file, and optionally a second
sequence file.
<li>entryname.idx is the entry name index. It has the same 300 byte
header, mainly used to store the record size which will depend on the
size of the longest entryname in the database. Each entry is stored in
sorted alphanumeric order so that a binary search can be used to
efficiently find any record. The record also holds the file number
from division.lkp and the offsets in the data and sequence files for
that entry.
<li>acnum.trg holds the accession number information. The file has the
usual 300 byte header, and a sorted list of record by accession number.
Each accession number record contains the first record number in acnum.hit
and the total number of records in acnum.hit so that secondary (duplicated)
accession numbers can be searched.
<li>acnum.hit is a very simple file. After the usual 300 byte header,
each record simply holds the record number in entryname.idx. An
accession number search will use acnum.trg to find a start position
and number of records to read in this file, and will then simply
read the entryname.idx records for each entry in turn.
</ul>
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
The indexing method depends on each entry having a unique entry name.
No allowance is made for two entries with the same name so it is
not possible to index EMBL and EMBLNEW together.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It exits with a status of 0 if no problems.
<H2>
Known bugs
</H2>
None.
<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="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="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>
<H2>
Author(s)
</H2>
Peter Rice (pmr © ebi.ac.uk)
<br>
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Completed December 1999
<H2>
Target users
</H2>
This program is intended to be used by administrators responsible
for software and database installation and maintenance.
<H2>
Comments
</H2>
None
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</HTML>
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