Datawraps are used by pyGeno to import data into it’s database. All reference genomes are downloaded from Ensembl, dbSNP data from dbSNP. The Bootstraping module has functions to import datawraps shipped with pyGeno. Datawraps can either be tar.gz.archives or folders.


Here’s how you import a reference genome datawrap:

from pyGeno.importation.Genomes import *

And a SNP set datawrap:

from pyGeno.importation.SNPs import *

Creating you own datawraps

For polymorphims, create a file called manifest.ini with the following format:

description = SNPs for testing purposes
maintainer = Tariq Daouda
maintainer_contact = tariq.daouda [at] umontreal
version = 1

species = human
name = mySNPSET
type = Agnostic # or CasavaSNP or dbSNPSNP
source = Where do these snps come from?

filename = snps.txt # or or if you chose not to include the file in the archive

And compress the manifest.ini file along sith the snps.txt (if you chose to include it and not to specify an url) into a tar.gz archive.

Natively pyGeno supports dbSNP and casava(snp.txt), but it also has its own polymorphism file format (AgnosticSNP) wich is simply a tab delemited file in the following format:

chromosomeNumber uniqueId   start        end      ref    alleles   quality       caller
        Y          1       2655643      2655644    T       AG        30          TopHat
        Y          2       2655645      2655647    -       AG        28          TopHat
        Y          3       2655648      2655650    TT      -         10          TopHat

Even tough all field are mandatory, the only ones that are critical for pyGeno to be able insert polymorphisms at the right places are: chromosomeNumber and start. All the other fields are non critical and can follow any convention you wish to apply to them, including the end field. You can choose the convention that suits best the query that you are planning to make on SNPs through .get(), or the way you intend to filter them using filtering objtecs.

For genomes, the manifet.ini file looks like this:

description = Test package. This package installs only chromosome Y of mus musculus
maintainer = Tariq Daouda
maintainer_contact = tariq.daouda [at] umontreal
version = GRCm38.73

species = Mus_musculus
name = GRCm38_test
source =

Y = Mus_musculus.GRCm38.73.dna.chromosome.Y.fa.gz # or an url such as ftp://... or http://

gtf = Mus_musculus.GRCm38.73_Y-only.gtf.gz # or an url such as ftp://... or http://

File URLs for refercence genomes can be found on Ensembl:

To learn more about datawraps and how to make your own you can have a look at Importation, and the Wiki.