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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="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>
Function
</H2>
Extract data from CUTG
<H2>
Description
</H2>
Given the name of a directory containing the CUTG database
(ftp://ftp.ebi.ac.uk/pub/databases/cutg) <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, will
create many files and take several minutes. The usage tables are from
the sum of codons over all sequences for each organism.
<p>
The EMBOSS distribution comes loaded with a set of codon usage tables.
Thes codon usage tables provided with the distribution are calculated
from the files 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.
<p>
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>. You should get all the
required *.codon files from CUTG, and uncompress them if they are
compressed before running <b>cutgextract</b> on them.
<p>
The task of downloading the CUTG database and running <b>cutgextract</b>
to create the codon usage table files from it would normally be done
only once when the EMBOSS package is being installled or if a new
version of the CUTG database is released.
<p>
Note by the way that CUTG has a drawback: it has a table for each organism
without making the distinction between different gene populations.
<p>
<H2>
Algorithm
</H2>
<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.
<p>
It then parses out the codon usage data from these *.codon files 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).
<H2>
Usage
</H2>
<b>Here is a sample session with cutgextract</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>cutgextract </b>
Extract data from CUTG
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>
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 is accepted)
-wildspec string [*.codon] Type of codon file (Any string is
accepted)
-species string [*] Species wildcard (Any string is
accepted)
-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 is accepted)
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory2 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>[-directory]<br>(Parameter 1)</td>
<td>Codon usage directories</td>
<td>Directory with files</td>
<td>.</td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>General log output file</td>
<td>Output file</td>
<td><i><*></i>.cutgextract</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>CUTG release</td>
<td>Any string is accepted</td>
<td><i>An empty string is accepted</i></td>
</tr>
<tr>
<td>-wildspec</td>
<td>Type of codon file</td>
<td>Any string is accepted</td>
<td>*.codon</td>
</tr>
<tr>
<td>-species</td>
<td>Species wildcard</td>
<td>Any string is accepted</td>
<td>*</td>
</tr>
<tr>
<td>-allrecords</td>
<td>Include all records, including those with warnings</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr>
<td>-filename</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 is accepted</td>
<td><i>An empty string is accepted</i></td>
</tr>
</table>
<H2>
Input file format
</H2>
<H2>
Output file format
</H2>
<b>cutgextract</b> outputs a set of EMBOSS codon usage data files to the EMBOSS
data/CODONS data directory
<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 EDictyostelium_discoideum.cut CDS: 7
Writing EAphrodite_aculeata.cut CDS: 1
Writing EAedes_aegypti.cut CDS: 23
Writing EAnadara_trapezia.cut CDS: 2
Writing EAedes_albopictus.cut CDS: 2
Writing EAcanthocheilonema_viteae.cut CDS: 2
Writing EAmblyomma_americanum.cut CDS: 2
Writing EAstacus_astacus.cut CDS: 3
Writing EAedes_atropalpus.cut CDS: 1
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
None
<H2>
Notes
</H2>
None.
<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 data from AAINDEX</td>
</tr>
<tr>
<td><a href="printsextract.html">printsextract</a></td>
<td>Extract data from PRINTS</td>
</tr>
<tr>
<td><a href="prosextract.html">prosextract</a></td>
<td>Build the PROSITE motif database for use by patmatmotifs</td>
</tr>
<tr>
<td><a href="rebaseextract.html">rebaseextract</a></td>
<td>Extract data from REBASE</td>
</tr>
<tr>
<td><a href="tfextract.html">tfextract</a></td>
<td>Extract data from TRANSFAC</td>
</tr>
</table>
<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>
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
</BODY>
</HTML>
|
