cutgextract

Function

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

Command line arguments


Input file format

Output file format

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

Data files

None

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Author(s)

History

Target users

Comments