cutgextract

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Function

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

% 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

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

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

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

History

Target users

Comments