Thanks for releasing this method for multiome data analysis.
transcripts = chd.biomart.get_transcripts(chd.biomart.Dataset.from_genome("GRCh38"), gene_ids=sample_transcriptome.var.index)
ValueError Traceback (most recent call last)
Cell In[10], line 1
----> 1 transcripts = chd.biomart.get_transcripts(chd.biomart.Dataset.from_genome("GRCh38"), gene_ids=sample_transcriptome.var.index)
2 fragments_file = "/public/home/xyy/LT_tmp_20241127/atac_rna/file/HCAHeart9508627_HCAHeart9508819/HCAHeart9508627_HCAHeart9508819_atac_fragments.tsv.gz"
3 transcripts = chd.data.regions.select_tss_from_fragments(transcripts, fragments_file)
File ~/miniconda3/envs/scVi/lib/python3.12/site-packages/chromatinhd/biomart/tss.py:100, in get_transcripts(biomart_dataset, gene_ids, symbols, chrom, start, end, filter_chromosomes, filter_protein_coding, batch_size)
86 attributes = [
87 biomart_dataset.attribute("ensembl_gene_id"),
88 biomart_dataset.attribute("transcript_start"),
(...)
96 biomart_dataset.attribute("transcript_biotype"),
97 ]
99 if len(filters) == 1:
--> 100 transcripts = biomart_dataset.get_batched(
101 attributes,
102 filters=filters,
103 )
104 else:
105 transcripts = biomart_dataset.get(attributes, filters=filters)
File ~/miniconda3/envs/scVi/lib/python3.12/site-packages/chromatinhd/biomart/dataset.py:216, in Dataset.get_batched(self, attributes, filters, batch_size, use_cache)
214 for i in tqdm.tqdm(range(0, len(filter), batch_size), leave=False):
215 filters_ = [filter[i : i + batch_size]]
--> 216 result.append(self.get(attributes=attributes, filters=filters_, use_cache=use_cache))
217 result = pd.concat(result)
218 return result
File ~/miniconda3/envs/scVi/lib/python3.12/site-packages/chromatinhd/biomart/dataset.py:189, in Dataset.get(self, attributes, filters, use_cache, timeout)
187 raise ValueError(response.text)
188 if "The Ensembl web service you requested is temporarily unavailable." in response.text:
--> 189 raise ValueError("Ensembl web service is temporarily unavailable")
190 result = pd.read_table(
191 io.StringIO(response.text),
192 sep="\t",
193 names=[attribute.name for attribute in attributes],
194 )
195 cache[url] = result
ValueError: Ensembl web service is temporarily unavailable
Thanks for releasing this method for multiome data analysis.
transcripts = chd.biomart.get_transcripts(chd.biomart.Dataset.from_genome("GRCh38"), gene_ids=sample_transcriptome.var.index)
ValueError Traceback (most recent call last)
Cell In[10], line 1
----> 1 transcripts = chd.biomart.get_transcripts(chd.biomart.Dataset.from_genome("GRCh38"), gene_ids=sample_transcriptome.var.index)
2 fragments_file = "/public/home/xyy/LT_tmp_20241127/atac_rna/file/HCAHeart9508627_HCAHeart9508819/HCAHeart9508627_HCAHeart9508819_atac_fragments.tsv.gz"
3 transcripts = chd.data.regions.select_tss_from_fragments(transcripts, fragments_file)
File ~/miniconda3/envs/scVi/lib/python3.12/site-packages/chromatinhd/biomart/tss.py:100, in get_transcripts(biomart_dataset, gene_ids, symbols, chrom, start, end, filter_chromosomes, filter_protein_coding, batch_size)
86 attributes = [
87 biomart_dataset.attribute("ensembl_gene_id"),
88 biomart_dataset.attribute("transcript_start"),
(...)
96 biomart_dataset.attribute("transcript_biotype"),
97 ]
99 if len(filters) == 1:
--> 100 transcripts = biomart_dataset.get_batched(
101 attributes,
102 filters=filters,
103 )
104 else:
105 transcripts = biomart_dataset.get(attributes, filters=filters)
File ~/miniconda3/envs/scVi/lib/python3.12/site-packages/chromatinhd/biomart/dataset.py:216, in Dataset.get_batched(self, attributes, filters, batch_size, use_cache)
214 for i in tqdm.tqdm(range(0, len(filter), batch_size), leave=False):
215 filters_ = [filter[i : i + batch_size]]
--> 216 result.append(self.get(attributes=attributes, filters=filters_, use_cache=use_cache))
217 result = pd.concat(result)
218 return result
File ~/miniconda3/envs/scVi/lib/python3.12/site-packages/chromatinhd/biomart/dataset.py:189, in Dataset.get(self, attributes, filters, use_cache, timeout)
187 raise ValueError(response.text)
188 if "The Ensembl web service you requested is temporarily unavailable." in response.text:
--> 189 raise ValueError("Ensembl web service is temporarily unavailable")
190 result = pd.read_table(
191 io.StringIO(response.text),
192 sep="\t",
193 names=[attribute.name for attribute in attributes],
194 )
195 cache[url] = result
ValueError: Ensembl web service is temporarily unavailable