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cutgextract |
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.
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).
% cutgextract Extract data from CUTG Codon usage directories [.]: data General log output file [outfile.cutgextract]: |
Go to the output files for this example
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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-directory] (Parameter 1) |
Codon usage directories | Directory with files | . |
| [-outfile] (Parameter 2) |
General log output file | Output file | <*>.cutgextract |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -release | CUTG release | Any string is accepted | An empty string is accepted |
| -wildspec | Type of codon file | Any string is accepted | *.codon |
| -species | Species wildcard | Any string is accepted | * |
| -allrecords | Include all records, including those with warnings | Boolean value Yes/No | No |
| -filename | 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 | An empty string is accepted |
This directory contains output files.
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 |
| 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 |