Mercurial > repos > xuebing > seq_shuffle_dinucleotide
changeset 0:aad0a5d475ce
Uploaded
| author | xuebing |
|---|---|
| date | Sat, 31 Mar 2012 21:47:42 -0400 |
| parents | |
| children | f9d894fb823c |
| files | seq_shuffle_dinucleotide.xml |
| diffstat | 1 files changed, 24 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seq_shuffle_dinucleotide.xml Sat Mar 31 21:47:42 2012 -0400 @@ -0,0 +1,24 @@ +<tool id="seq_shuffle_dinucleotide" name="shuffle sequence"> + <description>preserving dinucleotide frequency</description> + <command interpreter="python">fasta-dinucleotide-shuffle.py -f $input -t $tag -c $n -s $seed > $output </command> + <inputs> + <param name="input" format="fasta" type="data" label="Original sequence file"/> + <param name="tag" type="text" size="40" value="-shuffled" label="tag added to shuffled sequence name"/> + <param name="n" type="integer" value="1" label="number of shuffled copies for each sequence"/> + <param name="seed" type="integer" value="1" label="random seed" help="the same seed gives the same random sequences"/> + </inputs> + <outputs> + <data format="fasta" name="output" /> + </outputs> + <help> + +**What it does** + +This tool shuffles the sequences in the input file but preserves the dinucleotide frequency of each sequence. + +The code implements the Altschul-Erikson dinucleotide shuffle algorithm, described in "Significance of nucleotide sequence alignments: A method for random sequence permutation that preserves dinucleotide and codon usage", S.F. Altschul and B.W. Erikson, Mol. Biol. Evol., 2(6):526--538, 1985. + +Code adapted from http://bioinformatics.bc.edu/clotelab/RNAdinucleotideShuffle/dinucleotideShuffle.html + + </help> +</tool>