                                 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:6.6.0.0

   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


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      Process 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 (c) 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
