This is a simple Python package designed to allow kmers to be screened against a GenBank file, in this case H37Rv to see if they match.
If they do, the gemucator package is used to identify, if possible, the gene affected.
Since gemucator is not in PyPi, you will need to install it as per the instructions in the README on its GitHub page.
The only other pre-requsite is BioPython, which if not present, should be installed automatically during the below process.
First, clone the repository
$ git clone https://github.com/philipwfowler/kish
$ cd kish/
Now install either as a simple static package
$ python setup.py install --user
or, as a link if you anticipate updating the package via git pull frequently (do this way if the package is being developed and changed rapidly)
$ python setup.py develop --user
Fairly simple, you give it a kmer and it tells you if it can find it
$ kish-run.py --kmer CGGGGTTGACCCACAAGCGCCGACTGTCGGC
CGGGGTTGACCCACAAGCGCCGACTGTCGGC exactly matches forward starting at genbank location 761127 encoding rpoB_S441
It also considers all single base variants using a regular expression
$ kish-run.py --kmer CGGGGTTGACCCACAAGCGCCGACTGTCCGC
CGGGGTTGACCCACAAGCGCCGACTGTCCGC matches forward (C->G at pos 28) starting at genbank location 761127 encoding rpoB_S441
If you want to restrict it to exact matches then
$ kish-run.py --kmer CGGGGTTGACCCACAAGCGCCGACTGTCCGC --exact
CGGGGTTGACCCACAAGCGCCGACTGTCCGC no matches found!
- allow a file containing a kmer-per-line to be specified to increase speed/ease of use
- if a single base has been changed, work out what mutation in the reference genome that corresponds to
- can we think about 2 base changes? Or will that be too slow.