minor bugfix

bug fix when sample names contained ".fasta".
this was caused by using the string.split() method.

Zenodo release trigger

v.1.0.1

free version of pytables

lets get ready to rumble

based on the cookie cutter pypackage I've made many small changes in the codebase to be more compliant to pep8

pip installable!

Plasmidsimilarity is now installable from the repository using:

pip install .

describe the plasmids

this release contains additional workflow in the snakemake pipeline for description of the plasmids, such as number of contigs, total length and GC content

figures should now accommodate labels properly, thanks to Boas.
furthermore a composite plot is generated of the genotypes + similarity dendrogram.

release v0.4.0

release 0.4.0 has a lot of new stuff

• for the snakemake pipeline an output directory can be specified

• unique module added, which screens the fraction of unique k-mers over a range of k-mers

  • useful to determine if the size k you're using is big enough
  • furthermore it this plateaus before approaching 100% you'll know you have duplicated elements in your sequence

• code cleaning, Abricate rule in the snakefile is now a single rule for AMR plasmids and virulence genes.

small bug fix

now skips contigs smaller than size k

small fixes and code clean up

in this edition:

• circular plasmid k-mer counting
• code clean up how to read and k-mer count sequences

v0.1

Update README.md