gp_cusage - print codon usage of sequence(s)
gp_cusage [-c table_file ] [-p] [-q] [-v] [-d] [-h] [-?] [inputfile] [outputfile]
- -c table_file
- Uses alternate codon table.
- Nicely prints the codon table & exits gracefully.
- Prints the version information.
- Prints lots of debugging information.
- Shows usage information.
- file to proces; if not given, will use standard input
- file to write the data to; if not given, will use
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.
to print the codon usage of the fasta sequences contained in
the file orfs.fasta, type
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
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
The Genpak programs do not write over existing files. I have found this
feature very useful :-)
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.
January Weiner III