
                                cutgextract 



Function

   Extract data from CUTG

Description

   Given the name of a directory containing the CUTG database
   (ftp://ftp.ebi.ac.uk/pub/databases/cutg) 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, will create many files and take
   several minutes. The usage tables are from the sum of codons over all
   sequences for each organism.

   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
   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.

   You run cutgextract on the CUTG database from
   ftp://ftp.ebi.ac.uk/pub/databases/cutg. You should get all the
   required *.codon files from CUTG, and uncompress them if they are
   compressed before running cutgextract on them.

   The task of downloading the CUTG database and running cutgextract 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.

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

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 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).

Usage

   Here is a sample session with cutgextract


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

   Go to the output files for this example

Command line arguments

   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

Input file format

Output file format

   cutgextract outputs 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 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

Data files

   None

Notes

   None.

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 data from AAINDEX
   printsextract  Extract data from PRINTS
   prosextract    Build the PROSITE motif database for use by patmatmotifs
   rebaseextract  Extract data from REBASE
   tfextract      Extract data from TRANSFAC

Author(s)

   Alan Bleasby (ajb © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

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
