siblings 0.4.0

Siblings is a code base to compute homologs between genomes and make them publicly available through a REST api

How to install siblings

in principle, a - pip install -e . (from the repostitory root) should do the work. But unfortunately, the pytable package does not properly resolve all its dependencies. Hence, pytables needs to be already installed. See http://www.pytables.org/moin/Downloads for description (a longer version is contained in the documentation)

installing in ubuntu allows for: sudo apt-get install python-tables but depending on the ubuntu version, the package might be quite outdated.

instead, I used: sudo apt-get install libhdf5-serial-dev libbz2-dev liblzo2-dev pip install numpy pip install numexpr pip install cython pip install tables

and finally, install the siblings package - pip install -e .

Example session of direct siblings usage (not as a server)

import siblings

r = siblings.Reader(‘/path/to/master/file.h5’) genomes = r.genomes filterCond = siblings.QueryFilter(‘Score>500 & PamDistance<100’) idtype = r.createReturnIdType(‘UniProtKB/TrEMBL’,’SourceAC’) res = r.getMatchesBetweenGenomePair(genomes[1],genomes[2], matchFilter=filterCond, idType=idtype)

print(len(res[‘data’])) print(res[‘colnames’]) print(res[‘data’][0:10])

res = r.getHomologsOfGene(genomes[0],1,idType=idtype)