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ubuntu allows for: sudo apt-get install python-tables but depending on the ubuntu version, the package might be quite outdated.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

Release History

Release History


This version

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
siblings-0.4.0.tar.gz (304.3 kB) Copy SHA256 Checksum SHA256 Source May 21, 2015

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