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| "strand": -1, | |
| "gene_symbol": "RP4-669L17.2", | |
| "transcript_id": "ENST00000412666", | |
| "gene_id": "ENSG00000236601", | |
| "biotype": "lincRNA", | |
| "gene_symbol_source": "Clone_based_vega_gene", | |
| "consequence_terms": [ | |
| "transcript_amplification" | |
| ] | |
| }, | |
| { | |
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| "gene_symbol_source": "HGNC", | |
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| "upstream_gene_variant" | |
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| { | |
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| "biotype": "lincRNA", | |
| "gene_symbol_source": "Clone_based_vega_gene", | |
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| "transcript_amplification" | |
| ] | |
| }, | |
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| "gene_id": "ENSG00000237094", | |
| "biotype": "lincRNA", | |
| "gene_symbol_source": "Clone_based_vega_gene", | |
| "consequence_terms": [ | |
| "transcript_amplification" | |
| ] | |
| }, | |
| { | |
| "variant_allele": "duplication", | |
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| "strand": -1, | |
| "gene_symbol": "AP006222.1", | |
| "transcript_id": "ENST00000424429", | |
| "gene_id": "ENSG00000241670", | |
| "biotype": "processed_pseudogene", | |
| "gene_symbol_source": "Clone_based_vega_gene", | |
| "consequence_terms": [ | |
| "transcript_amplification" | |
| ] | |
| }, | |
| { | |
| "variant_allele": "duplication", | |
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| "bp_overlap": 7154, | |
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| "gene_symbol": "RP4-669L17.10", | |
| "transcript_id": "ENST00000440038", | |
| "gene_id": "ENSG00000237094", | |
| "biotype": "lincRNA", | |
| "gene_symbol_source": "Clone_based_vega_gene", | |
| "consequence_terms": [ | |
| "transcript_amplification" | |
| ] | |
| }, | |
| { | |
| "variant_allele": "duplication", | |
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| "bp_overlap": 13579, | |
| "strand": -1, | |
| "gene_symbol": "RP11-34P13.13", | |
| "transcript_id": "ENST00000466557", | |
| "gene_id": "ENSG00000241860", | |
| "biotype": "lincRNA", | |
| "gene_symbol_source": "Clone_based_vega_gene", | |
| "consequence_terms": [ | |
| "non_coding_exon_variant", | |
| "intron_variant", | |
| "nc_transcript_variant" | |
| ] | |
| }, | |
| { | |
| "variant_allele": "duplication", | |
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| "bp_overlap": 2806, | |
| "strand": -1, | |
| "gene_symbol": "CICP7", | |
| "transcript_id": "ENST00000432723", | |
| "gene_id": "ENSG00000233653", | |
| "canonical": 1, | |
| "biotype": "processed_pseudogene", | |
| "gene_symbol_source": "HGNC", | |
| "consequence_terms": [ | |
| "transcript_amplification" | |
| ] | |
| }, | |
| { | |
| "variant_allele": "duplication", | |
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| "strand": 1, | |
| "gene_symbol": "RP4-669L17.10", | |
| "transcript_id": "ENST00000419160", | |
| "gene_id": "ENSG00000237094", | |
| "biotype": "lincRNA", | |
| "gene_symbol_source": "Clone_based_vega_gene", | |
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| "transcript_amplification" | |
| ] | |
| }, | |
| { | |
| "variant_allele": "duplication", | |
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| "strand": 1, | |
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| "transcript_id": "ENST00000514436", | |
| "gene_id": "ENSG00000250575", | |
| "canonical": 1, | |
| "biotype": "unprocessed_pseudogene", | |
| "gene_symbol_source": "Clone_based_vega_gene", | |
| "consequence_terms": [ | |
| "transcript_amplification" | |
| ] | |
| }, | |
| { | |
| "variant_allele": "duplication", | |
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| "bp_overlap": 457, | |
| "strand": -1, | |
| "gene_symbol": "AP006222.1", | |
| "transcript_id": "ENST00000450734", | |
| "gene_id": "ENSG00000241670", | |
| "canonical": 1, | |
| "biotype": "processed_pseudogene", | |
| "gene_symbol_source": "Clone_based_vega_gene", | |
| "consequence_terms": [ | |
| "transcript_amplification" | |
| ] | |
| } | |
| ], | |
| "regulatory_feature_consequences": [ | |
| { | |
| "variant_allele": "duplication", | |
| "percentage_overlap": 87.67, | |
| "consequence_terms": [ | |
| "regulatory_region_variant" | |
| ], | |
| "bp_overlap": 576, | |
| "regulatory_feature_id": "ENSR00000278273" | |
| } | |
| ], | |
| "id": "sv1", | |
| "most_severe_consequence": "transcript_amplification", | |
| "start": 471362 | |
| } | |
| } |
Numbers which are strings are a problem with Perl and any text based transfer protocol. Perl says it doesn't care if it's a number until we want to eval it as one and then it'll do the checking/conversion. As @magaliruffier says it's a simple fix by just either doing +0 or *1 to any number.
As for the Boolean situation yes true is the correct way to represent this information. Our Json library does handle this via Types::Serialiser and it's true and false values. Though this does mean rewriting the output for a number of endpoints. I'm in favour of the change but this will have to be evaluated as to the impact of the change. If it's too large we should then schedule the change for the next major bump.
The reference allele should correspond to the first allele in your input (if searching by region), as well as the first allele in the allele_string field
in cases where the allele_string does not contain that information, we don't always know what the reference allele is
HGMD_mutation tells us there is a known mutation in the location, but we don't know what reference sequence they used, which might be different from our reference (refseq gene vs GRCh37 assembly for example)
We will look into adding the reference_allele field, but not in this implementation
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Great, thanks!
Would it be possible to include the reference allele as a separate field? It is usually present in
"allele_string": "A/G"but not always"allele_string": "HGMD_MUTATION"(although that is an odd one).