<html><head><title>gp_cusage</title>
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<h1>gp_cusage</h1>
<h2>GP</h2>
<h2>2000</h2>
<h2>NAME</h2>
gp_cusage - print codon usage of sequence(s)
<p><h2>SYNOPSIS</h2>
<strong>gp_cusage</strong> [-c table_file ] [-p] [-q] [-v] [-d] [-h] [-?] [inputfile] [outputfile]
<p><h2>OPTIONS</h2>
<p><dl>
<p><p></p><dt><strong>-c table_file</strong><dd> Uses alternate codon table.
<p><p></p><dt><strong>-p</strong><dd> Nicely prints the codon table & exits gracefully.
<p><p></p><dt><strong>-v</strong><dd> Prints the version information.
<p><p></p><dt><strong>-d</strong><dd> Prints lots of debugging information.
<p><p></p><dt><strong>-h</strong><dd> Shows usage information.
<p><p></p><dt><strong>inputfile</strong><dd> file to proces; if not given, will use standard input
<p><p></p><dt><strong>outputfile</strong><dd> file to write the data to; if not given, will use
standard output
<p></dl>
<p><h2>DESCRIPTION</h2>
<p><strong>gp_cusage</strong> 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.
<p><h2>EXAMPLES</h2>
<p><dl>
<p><li > to print the codon usage of the fasta sequences contained in
the file orfs.fasta, type
<p><code>gp_cusage orfs.fasta</code>
<p><li > to print the codon usage of a protein sequence located at
genome positions 15843 14602 in the sequence Mpneu.fasta, type
<p><code>getseq 15843 14602 Mpneu.fasta | gp_cusage</code>
<p></dl>
<p><h2>SEE ALSO</h2>
<a href="index.html">Genpak(1)</a>
<a href="gp_acc.html">gp_acc(1)</a>
<a href="gp_adjust.html">gp_adjust(1)</a>
<a href="gp_cdndev.html">gp_cdndev(1)</a>
<a href="gp_digest.html">gp_digest(1)</a>
<a href="gp_dimer.html">gp_dimer(1)</a>
<a href="gp_findorf.html">gp_findorf(1)</a>
<a href="gp_gc.html">gp_gc(1)</a>
<a href="gp_getseq.html">gp_getseq(1)</a>
<a href="gp_map.html">gp_map(1)</a>
<a href="gp_matrix.html">gp_matrix(1)</a>
<a href="gp_mkmtx.html">gp_mkmtx(1)</a>
<a href="gp_pattern.html">gp_pattern(1)</a>
<a href="gp_primer.html">gp_primer(1)</a>
<a href="gp_qs.html">gp_qs(1)</a>
<a href="gp_randseq.html">gp_randseq(1)</a>
<a href="gp_seq2prot.html">gp_seq2prot(1)</a>
<a href="gp_slen.html">gp_slen(1)</a>
<a href="gp_tm.html">gp_tm(1)</a>
<a href="gp_trimer.html">gp_trimer(1)</a>
<p><h2>DIAGNOSTICS</h2>
<p>All <strong>Genpak</strong> programs complain in situations you would also complain,
like when they cannot find a sequence you gave them or the sequence is not
valid.
<p>The <strong>Genpak</strong> programs do not write over existing files. I have found this
feature very useful :-)
<p><h2>BUGS</h2>
<p>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.
<p><h2>AUTHOR</h2>
<p>January Weiner III
<a href="mailto:january@bioinformatics.org"><january@bioinformatics.org></a>
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