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EMBOSS: cutgextract
cutgextract

 

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Function

Extract codon usage tables from CUTG database

Description

Given the name of a directory containing the CUTG database, cutgextract 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.

Algorithm

cutgextract 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.

Usage

Here is a sample session with cutgextract 


% cutgextract 
Extract codon usage tables from CUTG database
Codon usage directories [.]: data
General log output file [outfile.cutgextract]:

Go to the output files for this example

Command line arguments 

Extract codon usage tables from CUTG database
Version: EMBOSS:6.4.0.0

   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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-directory]
(Parameter 1)		 dirlist Codon usage directories Directory with files .
[-outfile]
(Parameter 2)		 outfile General log output file Output file <*>.cutgextract
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-release string CUTG release Any string  
-wildspec string Type of codon file Any string *.codon
-species string Species wildcard Any string *
-allrecords boolean Include all records, including those with warnings Boolean value Yes/No No
-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 dirlist qualifiers
-extension1
-extension_directory		 string Default file extension Any string  
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile		 string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

Output file format

cutgextract writes a set of EMBOSS codon usage data files to the EMBOSS data/CODONS data directory.

Output files for usage example

Directory: CODONS

This directory contains output files.

File: outfile.cutgextract

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

Data files

None

Notes

The EMBOSS distribution includes a set of codon usage tables calculated from the files listed in ftp://ftp.ebi.ac.uk/pub/databases/codonusage/README), 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 ftp://ftp.ebi.ac.uk/pub/databases/cutg.

If you run cutgextract on the CUTG database from ftp://ftp.ebi.ac.uk/pub/databases/cutg all of the *.codon files included in the database will be processed. You may need to uncompress these files (*.codon) before running cutgextract on them.

cutgextract would normally be used once when the EMBOSS package is installled, or when a new version of the CUTG database is released.

CUTG has a drawback: it has a table for each organism without making the distinction between different gene populations.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
aaindexextract Extract amino acid property data from AAINDEX
jaspextract Extract data from JASPAR
printsextract Extract data from PRINTS database for use by pscan
prosextract Processes the PROSITE motif database for use by patmatmotifs
rebaseextract Process the REBASE database for use by restriction enzyme applications
tfextract Process TRANSFAC transcription factor database for use by tfscan

Author(s)

Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Written (June 2001) - Alan Bleasby.

Target users

This program is intended to be used by administrators responsible for software and database installation and maintenance.

Comments

None