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ubuntu allows for: sudo apt-get install python-tables but depending on the ubuntu version, the package might be quite outdated.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)
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Release files for siblings 0.4.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
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| siblings-0.4.0.tar.gz | 304.3 kB | Details |
Release files / siblings-0.4.0.tar.gz
| Download URL | siblings-0.4.0.tar.gz |
|---|---|
| Size | 304.3 kB |
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