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

Project Description

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ubuntu allows for: sudo apt-get install python-tables but depending on the ubuntu version, the package might be quite outdated.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

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siblings-0.4.0.tar.gz (304.3 kB) Copy SHA256 hash SHA256 Source None May 21, 2015

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