cutgextract Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. 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:6.4.0.0 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 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 Processes 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