`getBM` won't return cdna and peptide together

[kwells4]

getBM won't return both cdna and peptide

When running getBM, It will correctly return results if cdna or peptide are requested as attributes, but not if both are requested. Below is an example

getBM returns cdna correctly

ensembl_hs <- biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl")

getBM(attributes = c("cdna", "hgnc_symbol",
                     "ensembl_transcript_id"), filters = list("hgnc_symbol" = "INS"),
      mart = ensembl_hs, checkFilters = FALSE, verbose = TRUE,
      useCache = TRUE)

cdna
1                                                                                                                                         CCAGCAGCCCTCAGCCCTCCAGGACAGGCTGCATCAGAAGAGGCCATCAAGCAGGTCTGTTCCAAGGGCCTTTGCGTCAGATCACTGTCCTTCTGCCATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGTACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAGACGCAGCCCGCAGGCAGCCCCACACCCGCCGCCTCCTGCACCGAGAGAGATGGAATAAAGCCCTTGAACCAGC
2 TCCAGGACAGGCTGCATCAGAAGAGGCCATCAAGCAGGTCTGTTCCAAGGGCCTTTGCGTCAGGTGGGCTCAGGATTCCAGGGTGGCTGGACCCCAGGCCCCAGCTCTGCAGCAGGGAGGACGTGGCTGGGCTCGTGAAGCATGTGGGGGTGAGCCCAGGGGCCCCAAGGCAGGGCACCTGGCCTTCAGCCTGCCTCAGCCCTGCCTGTCTCCCAGATCACTGTCCTTCTGCCATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGTACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAGACGCAGCCCGCAGGCAGCCCCACACCCGCCGCCTCCTGCACCGAGAGAGATGGAATAAAGCCCTTGAACCAGC
3                                                                                                                                                                               AGCCCTCCAGGACAGGCTGCATCAGAAGAGGCCATCAAGCAGATCACTGTCCTTCTGCCATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGTGGGGCAGGTGGAGCTGGGCGGGGGCCCTGGTGCAGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGTACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAGACGCAGCCCGCAGGCAGCCCCACACCCGCCGCCTCCTGCACCGAGAGAGATGGAATAAAGCCCTTGAACCAGC
4                                                                                                                                                                                AAGGGCCTTTGCGTCAGGTGGGCTCAGGATTCCAGGGTGGCTGGACCCCAGGCCCCAGCTCTGCAGCAGGGAGGACGTGGCTGGGCTCGTGAAGCATGTGGGGGTGAGCCCAGGGGCCCCAAGGCAGGGCACCTGGCCTTCAGCCTGCCTCAGCCCTGCCTGTCTCCCAGATCACTGTCCTTCTGCCATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGCTGGAGAACTACTGCAACTAGACGCAGCCCGCAGGCAGCCCCACACCCGCCGCCTCCTGCACCGAGAGAGATGGAATAAAGCCCTTGAAC
5                                                                                                                                                                                                                                                                                                                                                       ATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTGGCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAGCTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCTGCAGGGCAGCCTGCAGCCCTTGGCCCTGGAGGGGTCCCTGCAGAAGCGTGGCATTGTGGAACAATGCTGTACCAGCATCTGCTCCCTCTACCAGCTGGAGAACTACTGCAACTAG
  hgnc_symbol ensembl_transcript_id
1         INS       ENST00000250971
2         INS       ENST00000397262
3         INS       ENST00000381330
4         INS       ENST00000421783
5         INS       ENST00000512523

getBM returns peptide correctly

ensembl_hs <- biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl")

getBM(attributes = c("peptide", "hgnc_symbol",
                     "ensembl_transcript_id"), filters = list("hgnc_symbol" = "INS"),
      mart = ensembl_hs, checkFilters = FALSE, verbose = TRUE,
      useCache = TRUE)

 peptide
1 MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN*
2 MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN*
3 MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN*
4                    MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQAGELLQLDAARRQPHTRRLLHRERWNKALE
5             MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN*
  hgnc_symbol ensembl_transcript_id
1         INS       ENST00000397262
2         INS       ENST00000250971
3         INS       ENST00000381330
4         INS       ENST00000421783
5         INS       ENST00000512523

getBM fails with both

ensembl_hs <- biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl")

getBM(attributes = c("peptide", "cdna", "hgnc_symbol",
                     "ensembl_transcript_id"), filters = list("hgnc_symbol" = "INS"),
      mart = ensembl_hs, checkFilters = FALSE, verbose = TRUE,
      useCache = TRUE)

                  cdna peptide     hgnc_symbol ensembl_transcript_id
1 Sequence unavailable     INS ENST00000421783             HGNC:6081
2 Sequence unavailable     INS ENST00000250971             HGNC:6081
3 Sequence unavailable     INS ENST00000381330             HGNC:6081
4 Sequence unavailable     INS ENST00000397262             HGNC:6081
5 Sequence unavailable     INS ENST00000512523             HGNC:6081

I also see behavior similar to what is described in #108 where the column headers no longer match and I am getting attributes returned that I did not request. Any idea why it works with each individually but not together?

[grimbough]

I think the answer to this is the same as in #109. In the web interface the peptide and cdna attributes are radio buttons and you can't select both of them.

Unfortunately the BioMart API doesn't provide any way to detect which attributes are mutually exclusive like this, so I can't detect and filter it in biomaRt. It seem the server is also happy to run a query, even if what comes back doesn't reflect exactly what was asked for.

The getSequence() function does a similar job to what you're looking for and will fail if you ask for more than one sequence type, but I'm not sure there's anyway I can catch this in generic calls to getBM(). I think it's an issue server side to even allow a query like this to run if it isn't viable.