dipper.sources.Bgee module¶
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class
dipper.sources.Bgee.Bgee(graph_type, are_bnodes_skolemized, data_release_version=None, tax_ids=None, version=None)¶ Bases:
dipper.sources.Source.SourceBgee is a database to retrieve and compare gene expression patterns between animal species.
Bgee first maps heterogeneous expression data (currently RNA-Seq, Affymetrix, in situ hybridization, and EST data) to anatomy and development of different species.
Then, in order to perform automated cross species comparisons, homology relationships across anatomies, and comparison criteria between developmental stages, are designed.
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check_if_remote_is_newer(localfile, remote_size, remote_modify)¶ Overrides check_if_remote_is_newer in Source class
Parameters: - localfile – str file path
- remote_size – str bytes
- remote_modify – str last modify date in the form 20160705042714
Returns: boolean True if remote file is newer else False
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default_species= ['Cavia porcellus', 'Mus musculus', 'Rattus norvegicus', 'Monodelphis domestica', 'Anolis carolinensis', 'Caenorhabditis elegans', 'Drosophila melanogaster', 'Danio rerio', 'Xenopus (Silurana) tropicalis', 'Gallus gallus', 'Ornithorhynchus anatinus', 'Erinaceus europaeus', 'Macaca mulatta', 'Gorilla gorilla', 'Pan paniscus', 'Pan troglodytes', 'Homo sapiens', 'Canis lupus familiaris', 'Felis catus', 'Equus caballus', 'Sus scrofa', 'Bos taurus', 'Oryctolagus cuniculus']¶
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fetch(is_dl_forced=False)¶ Parameters: is_dl_forced – boolean, force download Returns:
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files= {'anat_entity': {'columns': ['Ensembl gene ID', 'gene name', 'anatomical entity ID', 'anatomical entity name', 'rank score', 'XRefs to BTO'], 'path': '/download/ranks/anat_entity/', 'pattern': re.compile('^[0-9]+_anat_entity_all_data_.*.tsv.gz')}}¶
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parse(limit=None)¶ Given the input taxa, expects files in the raw directory with the name {tax_id}_anat_entity_all_data_Pan_troglodytes.tsv.zip
Parameters: limit – int Limit to top ranked anatomy associations per group Returns: None
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