def _get_available_organisms(self):
available_organism = sorted([(tax_id, taxonomy.name(tax_id))
for tax_id in taxonomy.common_taxids()],
key=lambda x: x[1])
self.organisms = [tax_id[0] for tax_id in available_organism]
self.organism_select_combobox.addItems(
[tax_id[1] for tax_id in available_organism])
def register_serverfiles(genesets):
""" Registers using the common hierarchy and organism. """
org = genesets.common_org()
hierarchy = genesets.common_hierarchy()
fn = filename(hierarchy, org)
file_path = os.path.join(DOMAIN_PATH, fn)
if org is not None:
taxname = taxonomy.name(org)
title = "Gene sets: " + ", ".join(hierarchy) + (
(" (" + taxname + ")") if org is not None else "")
tags = list(hierarchy) + ["gene sets"] + (
[taxname] if org is not None else []) + taxonomy.shortname(org)
genesets.to_gmt_file_format(file_path)
create_info_file(file_path, title=title, tags=tags)
def kegg_gene_sets(tax_id: str) -> None:
""" Returns gene sets from KEGG pathways.
"""
caching.clear_cache()
kegg_org = kegg.KEGGOrganism(taxonomy.name(tax_id))
ncbi_id_mapper = kegg_org.kegg_to_ncbi_mapper()
genesets = []
for id in kegg_org.pathways():
pway = kegg.KEGGPathway(id)
hier = ('KEGG', 'Pathways')
if pway.pathway_attributes():
kegg_names = kegg_org.get_genes_by_pathway(id)
mapped_genes = set()
for gene in kegg_names:
try:
mapped_genes.add(ncbi_id_mapper[gene.upper()])
except KeyError:
# some kegg names can not be matched to ncbi ids
# they are included in geneset anyway
# remove prefix, that specifies kegg organism
# mapped_genes.append(gene.split(':')[-1])
pass
gs = GeneSet(gs_id=id,
name=pway.title,
genes=mapped_genes,
hierarchy=hier,
organism=tax_id,
link=pway.link)
genesets.append(gs)
for gs_group in GeneSets(genesets).split_by_hierarchy():
hierarchy = gs_group.common_hierarchy()
gs_group.to_gmt_file_format(
f'{data_path}/gene_sets/{filename(hierarchy, tax_id)}')
def listAvailable():
taxids = taxonomy.common_taxids()
essential = [(taxonomy.name(taxid), 'gene_association.{}'.format(taxid)) for taxid in taxids
if (DOMAIN, 'gene_association.{}'.format(taxid)) in serverfiles.ServerFiles().listfiles(DOMAIN)]
return dict(essential)
def setUp(self):
self.common_ids = taxonomy.common_taxids()
self.organisms = [(taxonomy.name(tax_id), tax_id)
for tax_id in self.common_ids]
self.taxon = taxonomy.Taxonomy()