Entering edit mode
2.2 years ago
ngarber
▴
60
I'm trying to get yeast and human protein sequences, and the human one works, but yeast doesn't - anyone know what's going on? Here is my code:
>>> server = pybiomart.Server(host="http://www.ensembl.org")
>>> mart = server["ENSEMBL_MART_ENSEMBL"]
>>> hsapiens_dataset = mart["hsapiens_gene_ensembl"]
>>> scerevisiae_dataset = mart["scerevisiae_gene_ensembl"]
>>> hsapiens_df = hsapiens_dataset.query(attributes = ["ensembl_peptide_id", "peptide"])
>>> hsapiens_df
Peptide Protein stable ID
0 MAAAAGMLLLGLLQAGGSVLGQAMEKVTGGNLLSMLLIACAFTLSL... ENSP00000003100
1 MAALLLGAVLLVAQPQLVPSRPAELGQQELLRKAGTLQDDVRDGVA... ENSP00000002596
2 MTLLTFRDVAIEFSLEEWKCLDLAQQNLYRDVMLENYRNLFSVGLT... ENSP00000005082
3 MLLGELGVFASYAFAPLSLIVPLSAVSVIASAIIGIIFIKEKWKPK... ENSP00000003912
4 MTAELQQDDAAGAADGHGSSCQMLLNQLREITGIQDPSFLHEALKA... ENSP00000003302
... ... ...
120708 MRLDNMLLAEGVAGPEKGGGSAAAAAAAAASGGAGSDNSVEHSDYR... ENSP00000514644
120709 MGTTASTAQQTVSAGTPFEGLQGSGTMDSRHSVSIHSFQSTSLHNS... ENSP00000513343
120710 XTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKT... ENSP00000513219
120711 MRTEDLPKAVVFLEPQWYRVLEKDSVTLKCQGAYSPEDNSTQWFHN... ENSP00000514360
120712 MADEKPSNGVLVHMVKLLIKTFLDGIFDDLMENNVLNTDEIHLIGK... ENSP00000515267
[120713 rows x 2 columns]
>>> scerevisiae_df = scerevisiae_dataset.query(attributes = ["ensembl_peptide_id", "peptide"])
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/tiltwolf/.local/lib/python3.10/site-packages/pybiomart/dataset.py", line 266, in query
raise BiomartException(response.text)
pybiomart.base.BiomartException: Query ERROR: caught BioMart::Exception::Query: returning undef ... missing attributes for your exportable?
Update: there appears to be an error on BioMart's end, because I get the same error if I try to query the peptide sequence through the BioMart website. Is it happening for others?
