bioDBs is a Python package for getting data from biological databases.
Project description
bioDBs
bioDBs is a Python package for getting data from biological databases.
List of the databases
- BioMart
- KEGG
- QuickGO
- HPA
How to use
BioMart
from biodbs import BioMart
ds = BioMart.Dataset(dataset_name="hsapiens_gene_ensembl")
ds.get_data(attribs=["ensembl_gene_id",
"ensembl_transcript_id",
"entrezgene_id",
"hgnc_symbol",
"uniprotswissprot"],
ensembl_gene_id=["ENSG00000139618", "ENSG00000272104"])
KEGG
from biodbs import KEGG
# list available databases
KEGG.list_database()
kegg = KEGG.KEGGdb()
# get entry links
kegg.list_entry_link(target_db="pathway", source_db="hsa")
QuickGO
from biodbs import QuickGO
qgo = QuickGO.QuickGOdb()
# search by text and list the results
qgo.list_search_result("mito")
# save a GO-term tree chart
qgo.save_chart(["GO:1903695", "GO:1904922", "GO:0000423", "GO:0042645"], "test.png")
Human Protein Atlas (HPA)
from biodbs import HPA
hpa = HPA.HPAdb()
# list downloadable tsv files
print(HPA.DOWNLOADABLE_DATA)
# download tsv file from HPA
hpa.download_HPA_data("normal_tissue", saved_path="./")
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