Pre-defined sources reference

Predefined sources are specified in ibidas.pre. They can be accessed through get, e.g.:

>>> feats = get.yeast_orfs()

class ibidas.pre.Pre

register(func, name=None, category=None)

ibidas.pre.biogrid(orgs=None)

Download the biogrid dataset. orgs is an array which specifies which organism(s) you want. e.g.

bg = Get.biogrid([‘Saccharomyces cerevisiae’])

Returns the biogrid data for Yeast only.

ibidas.pre.extract_info(vals)

ibidas.pre.file_db(filename)

Returns an empty in memory database

ibidas.pre.get_kegg_btit(names)

ibidas.pre.get_kegg_organisms()

ibidas.pre.get_kegg_pathway(pathway)

ibidas.pre.get_kegg_pathways(org)

ibidas.pre.go_annotations(dburl='mysql://dbl:dissimilarity@inpc09.et.tudelft.nl/go', genus='Saccharomyces', species='cerevisiae', include_ancestors=False)

Accesses GO annotations in a MySQL database.

Database data can be obtained from the geneontology website.

example url: “mysql://username:password@hostname:port/go

ibidas.pre.go_info(dburl='mysql://dbl:dissimilarity@inpc09.et.tudelft.nl/go', genus='Saccharomyces', species='cerevisiae', include_ancestors=False)

Accesses GO term info in a MySQL database.

Database data can be obtained from the geneontology website.

example url: “mysql://username:password@hostname:port/go

ibidas.pre.in_memory_db()

Returns an empty in memory database

ibidas.pre.omim_disease_parse(x)

ibidas.pre.omim_genemap()

The omim genemap data

ibidas.pre.string_interaction_types(dburl='postgresql://string:interactionshere@adara.et.tudelft.nl:5400/string', species='Saccharomyces cerevisiae', external_names=False)

Given a Postgres db with String data, specified in dburl, and a species, returns all interactions and their score.

The database data can be obtained from String.

example url: “postgres://username:password@hostname:port/string_dbname”

Use connect to access the whole database:

#Get available species names: 
>>> connect(dburl).items.species.offical_name

ibidas.pre.string_interactions(dburl='postgresql://string:interactionshere@adara.et.tudelft.nl:5400/string', species='Saccharomyces cerevisiae', subscores=False, external_names=False)

Given a Postgres db with String data, specified in dburl, and a species, returns all interactions and their score.

The database data can be obtained from String.

example url: “postgres://username:password@hostname:port/string_dbname”

Use connect to access the whole database:

#Get available species names: 
>>> connect(dburl).items.species.offical_name

ibidas.pre.yeast_aliases(feats, remove_multi=True)

Given a yeast feats table (see yeast_feats), returns a two column table with aliases and the corresponding official feature names. All names in output are in uppercase.

Parameters:remove_multi – if True (default), removes aliases that map to multiple offical feature names.

ibidas.pre.yeast_chipchip(translator=None)

ibidas.pre.yeast_collins_genetic()

ibidas.pre.yeast_collins_physical()

ibidas.pre.yeast_feats()

Returns table of yeast genome features, from: http://downloads.yeastgenome.org/curation/chromosomal_feature/SGD_features.tab

ibidas.pre.yeast_kinome()

ibidas.pre.yeast_phosphogrid()

ibidas.pre.yeastract(translator=None, url='http://www.yeastract.com/download/RegulationTwoColumnTable_Documented_20111009.tsv.gz')

Downloads documented transcription factor regulation interactions from yeastract