Py-DCJ is a python implementation of a distance algorithm based on the double-cut and join (DCJ) model of genome rearrangements. DCJ is an abstract operation on sets of linear and circular chromosomes defined by cutting the genome in 2 locations and rejoining the ends. General information about the model can be found on the wikipedia page.
Chromosome representation under the DCJ model is a list of unique markers representing "genes" or a block of dna. Linear chromosomes are denoted with a telomere "." at each end of the chromosomes, while circular chromosomes do not have telomeres. Genomes are represented as lists of chromosomes.
For example [".abcD.", "eF"] is a genome with 1 linear and 1 circular chromosome. Each unique marker is a single letter. Capital letters indicate that the gene is in reverse orientation.
Py-DCJ can calculate distances based on common markers between the two genomes (default method: dcj) , or including insertion-deletion (indel) information. For more details about the distance algorithm, see this paper.
>>> from dcj.main import calculate_distance
>>> genome_a = [".abc."]
>>> genome_b = [".aCBd."]
>>> calculate_distance(genome_a, genome_b, method="dcj")
... 1.0
>>> caculate_distance(genome_a, genome_b, method="indel")
... 2.0
The recommended way to install Py-DCJ is via git clone.