gp_cusage
GP
2000
NAME
gp_cusage - print codon usage of sequence(s)
SYNOPSIS
gp_cusage [-c table_file ] [-p] [-q] [-v] [-d] [-h] [-?] [inputfile] [outputfile]
OPTIONS
- -c table_file
- Uses alternate codon table.
- -p
- Nicely prints the codon table & exits gracefully.
- -v
- Prints the version information.
- -d
- Prints lots of debugging information.
- -h
- Shows usage information.
- inputfile
- file to proces; if not given, will use standard input
- outputfile
- file to write the data to; if not given, will use
standard output
DESCRIPTION
gp_cusage sources one or more DNA or RNA sequence files and prints the
total percentual frequencies of all codons. The sequences have to begin
with a start codon, but if they are incomplete (i.e. end before the
stop codon is read) only a warning is issued.
EXAMPLES
to print the codon usage of the fasta sequences contained in
the file orfs.fasta, type
gp_cusage orfs.fasta
to print the codon usage of a protein sequence located at
genome positions 15843 14602 in the sequence Mpneu.fasta, type
getseq 15843 14602 Mpneu.fasta | gp_cusage
SEE ALSO
Genpak(1)
gp_acc(1)
gp_digest(1)
gp_dimer(1)
gp_findorf(1)
gp_gc(1)
gp_getseq(1)
gp_map(1)
gp_matrix(1)
gp_mkmtx(1)
gp_pattern(1)
gp_primer(1)
gp_qs(1)
gp_randseq(1)
gp_seq2prot(1)
gp_slen(1)
gp_tm(1)
gp_trimer(1)
DIAGNOSTICS
All Genpak programs complain in situations you would also complain,
like when they cannot find a sequence you gave them or the sequence is not
valid.
The Genpak programs do not write over existing files. I have found this
feature very useful :-)
BUGS
I'm sure there are plenty left, so please mail me if you find them. I tried
to clean up every bug I could find.
AUTHOR
January Weiner III
<january@bioinformatics.org>