def send_to_output(self, result):
self.progress_bar.finish()
self.setStatusMessage('')
etc_json, table_name = result
# convert to table
data = etc_to_table(etc_json, bool(self.gene_as_attr_name))
# set table name
data.name = table_name
# match genes
gene_matcher = GeneMatcher(str(self.organism))
if not bool(self.gene_as_attr_name):
if 'Gene' in data.domain:
data = gene_matcher.match_table_column(
data, 'Gene', StringVariable(ENTREZ_ID))
data.attributes[GENE_ID_COLUMN] = ENTREZ_ID
else:
gene_matcher.match_table_attributes(data)
data.attributes[GENE_ID_ATTRIBUTE] = ENTREZ_ID
# add table attributes
data.attributes[TAX_ID] = str(self.organism)
data.attributes[GENE_AS_ATTRIBUTE_NAME] = bool(self.gene_as_attr_name)
# reset cache indicators
self.set_cached_indicator()
# send data to the output signal
self.Outputs.etc_data.send(data)
def test_match_table_column(self):
gm = GeneMatcher('4932')
data = gm.match_table_column(Table('brown-selected.tab'), 'gene')
self.assertTrue(ENTREZ_ID in data.domain)
def panglao_db(file_path: str):
file_name = 'panglao_gene_markers.tab'
reference, reference_url = 'PanglaoDB', 'https://panglaodb.se/'
with gzip.open(file_path, 'rb') as f:
content = f.read().decode('utf-8').strip()
species = 0
gene_symbol = 1
cell_type = 2
genes_by_organism = defaultdict(list)
organism_mapper = {'Mm': 'Mouse', 'Hs': 'Human'}
def _gene_function_table(desc_col: StringVariable,
gm_results: GeneMatcher):
_domain = Domain([], metas=[desc_col])
_data = [[str(gene.description) if gene.description else '']
for gene in gm_results.genes]
return Table(_domain, _data)
for line in content.split('\n'):
columns = line.split('\t')
for org in columns[species].split(' '):
if org in organism_mapper.keys():
gene_entry = [
organism_mapper[org], columns[gene_symbol],
columns[cell_type], reference, reference_url
]
genes_by_organism[organism_mapper[org]].append(gene_entry)
domain = Domain(
[],
metas=[
StringVariable('Organism'),
StringVariable('Name'),
StringVariable('Cell Type'),
StringVariable('Reference'),
StringVariable('URL'),
],
)
entrez_id_column = StringVariable('Entrez ID')
description_column = StringVariable('Function')
# construct data table for mouse
gm_mouse = GeneMatcher('10090')
mouse_table = Table(domain, genes_by_organism['Mouse'])
mouse_table = gm_mouse.match_table_column(mouse_table, 'Name',
entrez_id_column)
mouse_table = Table.concatenate(
[mouse_table,
_gene_function_table(description_column, gm_mouse)])
# construct data table for human
gm_human = GeneMatcher('9606')
human_table = Table(domain, genes_by_organism['Human'])
human_table = gm_human.match_table_column(human_table, 'Name',
entrez_id_column)
human_table = Table.concatenate(
[human_table,
_gene_function_table(description_column, gm_human)])
# return combined tables
Table.concatenate([mouse_table, human_table],
axis=0).save(f'data/marker_genes/{file_name}')
