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<HTML>
<HEAD>
<TITLE>
EMBOSS: cutgextract
</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="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
cutgextract
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Wiki
</H2>
The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.
<p>
Please help by correcting and extending the Wiki pages.
<H2>
Function
</H2>
Extract codon usage tables from CUTG database
<H2>
Description
</H2>
<p>Given the name of a directory containing the CUTG database, <b>cutgextract</b> will calculate codon usage tables for individual species (e.g. EHomo_sapiens.cut) and place them in the CODONS subdirectory of the EMBOSS data directory. This is an all-or-nothing extraction; it will create many files and take several minutes. The usage tables are calculated from the sum of codons over all sequences for each organism.</p>
<H2>
Algorithm
</H2>
<p><b>cutgextract</b> looks in the specified directory and opens all the files with the extension '.codon'. These are all expected to be CUTG data files. It then parses out the codon usage data and writes one file per species into the EMBOSS data/CODONS directory. The names of the files are derived from the species names in the CUTG files. These files names will be long and therefore descriptive.</p>
<H2>
Usage
</H2>
Here is a sample session with <b>cutgextract</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>cutgextract </b>
Extract codon usage tables from CUTG database
Codon usage directories [.]: <b>data</b>
General log output file [outfile.cutgextract]: <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>
Extract codon usage tables from CUTG database
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-directory] dirlist [.] Codon usage directories
[-outfile] outfile [*.cutgextract] General log output file
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-release string CUTG release (Any string)
-wildspec string [*.codon] Type of codon file (Any string)
-species string [*] Species wildcard (Any string)
-allrecords boolean [N] Include all records, including those
with warnings
-filename string Single output filename to override automatic
one file for each species. Leave blank to
generate the filenames. Specify a filename
to combine several species into one file.
(Any string)
Associated qualifiers:
"-directory" associated qualifiers
-extension1 string Default file extension
"-outfile" associated qualifiers
-odirectory2 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to 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 and exit. 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
-version boolean Report version number and exit
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>
<tr bgcolor="#FFFFCC">
<td>[-directory]<br>(Parameter 1)</td>
<td>dirlist</td>
<td>Codon usage directories</td>
<td>Directory with files</td>
<td>.</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 2)</td>
<td>outfile</td>
<td>General log output file</td>
<td>Output file</td>
<td><i><*></i>.cutgextract</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>
<tr>
<td colspan=5>(none)</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>
<tr bgcolor="#FFFFCC">
<td>-release</td>
<td>string</td>
<td>CUTG release</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-wildspec</td>
<td>string</td>
<td>Type of codon file</td>
<td>Any string</td>
<td>*.codon</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-species</td>
<td>string</td>
<td>Species wildcard</td>
<td>Any string</td>
<td>*</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-allrecords</td>
<td>boolean</td>
<td>Include all records, including those with warnings</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-filename</td>
<td>string</td>
<td>Single output filename to override automatic one file for each species. Leave blank to generate the filenames. Specify a filename to combine several species into one file.</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>
<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-directory" associated dirlist qualifiers
</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -extension1<br>-extension_directory</td>
<td>string</td>
<td>Default file extension</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -odirectory2<br>-odirectory_outfile</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td> </td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>
<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>
</table>
<H2>
Input file format
</H2>
<H2>
Output file format
</H2>
<p><b>cutgextract</b> writes a set of EMBOSS codon usage data files to the EMBOSS data/CODONS data directory.</p>
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>Directory: CODONS</h3>
<p>This directory contains output files.
<p>
<p><h3>File: outfile.cutgextract</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Writing EAphrodite_aculeata.cut CDS: 1
Writing EAnadara_trapezia.cut CDS: 2
Writing EAcanthocheilonema_viteae.cut CDS: 2
Writing EAedes_aegypti.cut CDS: 23
Writing EDictyostelium_discoideum.cut CDS: 7
Writing EAmblyomma_americanum.cut CDS: 2
Writing EAedes_atropalpus.cut CDS: 1
Writing EAedes_albopictus.cut CDS: 2
Writing EAstacus_astacus.cut CDS: 3
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
None
<H2>
Notes
</H2>
<p>The EMBOSS distribution includes a set of codon usage tables calculated from the files listed in <a href="ftp://ftp.ebi.ac.uk/pub/databases/codonusage/README">ftp://ftp.ebi.ac.uk/pub/databases/codonusage/README</a>), with a few additions whose exact derivation cannot easily be determined. Many people would prefer to create their own from the public CUTG data. The CUTG database can be downloaded from <a href="ftp://ftp.ebi.ac.uk/pub/databases/cutg">ftp://ftp.ebi.ac.uk/pub/databases/cutg</a>.</p>
<p>If you run <b>cutgextract</b> on the CUTG database from <a href="ftp://ftp.ebi.ac.uk/pub/databases/cutg">ftp://ftp.ebi.ac.uk/pub/databases/cutg</a> all of the *.codon files included in the database will be processed. You may need to uncompress these files (<tt>*.codon</tt>) before running <b>cutgextract</b> on them.</p>
<p><b>cutgextract</b> would normally be used once when the EMBOSS package is installled, or when a new version of the CUTG database is released.</p>
<p>CUTG has a drawback: it has a table for each organism without making the distinction between different gene populations.</p>
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with status 0.
<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="aaindexextract.html">aaindexextract</a></td>
<td>Extract amino acid property data from AAINDEX</td>
</tr>
<tr>
<td><a href="jaspextract.html">jaspextract</a></td>
<td>Extract data from JASPAR</td>
</tr>
<tr>
<td><a href="printsextract.html">printsextract</a></td>
<td>Extract data from PRINTS database for use by pscan</td>
</tr>
<tr>
<td><a href="prosextract.html">prosextract</a></td>
<td>Process the PROSITE motif database for use by patmatmotifs</td>
</tr>
<tr>
<td><a href="rebaseextract.html">rebaseextract</a></td>
<td>Process the REBASE database for use by restriction enzyme applications</td>
</tr>
<tr>
<td><a href="tfextract.html">tfextract</a></td>
<td>Process TRANSFAC transcription factor database for use by tfscan</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Alan Bleasby
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<p>
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
<H2>
History
</H2>
Written (June 2001) - Alan Bleasby.
<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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