Bootstraping

pyGeno can be quick-started by importing these built-in data wraps.

bootstrap.importGenome(name, batchSize=100)[source]

Import a genome shipped with pyGeno. Most of the datawraps only contain URLs towards data provided by third parties.

bootstrap.importRemoteGenome(name, batchSize=100)[source]

Import a genome available from http://pygeno.iric.ca (might work).

bootstrap.importRemoteSNPs(name)[source]

Import a SNP set available from http://pygeno.iric.ca (might work).

bootstrap.importSNPs(name)[source]

Import a SNP set shipped with pyGeno. Most of the datawraps only contain URLs towards data provided by third parties.

bootstrap.listDatawraps()[source]

Lists all the datawraps pyGeno comes with

bootstrap.listRemoteDatawraps(location='http://bioinfo.iric.ca/~daoudat/pyGeno_datawraps')[source]

Lists all the datawraps availabe from a remote a remote location.

bootstrap.printDatawraps()[source]

print all available datawraps for bootstraping

bootstrap.printRemoteDatawraps(location='http://bioinfo.iric.ca/~daoudat/pyGeno_datawraps')[source]

print all available datawraps from a remote location the location must have a datawraps.json in the following format:

{
"Ordered": {
        "Reference genomes": {
                "Human" :       ["GRCh37.75", "GRCh38.78"],
                "Mouse" : ["GRCm38.78"],
        },
        "SNPs":{
                }
},
"Flat":{
        "Reference genomes": {
                "GRCh37.75": "Human.GRCh37.75.tar.gz",
                "GRCh38.78": "Human.GRCh37.75.tar.gz",
                "GRCm38.78": "Mouse.GRCm38.78.tar.gz"
        },
        "SNPs":{
        }
}

}