[ensembl-dev] Fwd: Inconsistent results when making POST requests to grch37 / variant_recoder

[Diana Lemos]

Hi Josh,

The problem is the HGVS 'NM_000070.2:c.?' this notation is not supported 
and it also contains the character '?' which is causing the output 
problems. If you try the same code without this HGVS the code should 
have the expected output.


Best wishes,

Diana


> Dear Ensembl team,
>    I'd like some help with this. I am interested in using 
> https://grch37.rest.ensembl.org/documentation/info/variant_recoder_post in 
> obtaining VCF coordinates for a number of variants ( Input being HGVS 
> coordinates)
>
> I used the Python 3 sample code provided to check what the resulting 
> output looks like (pasted further below)
>
> In similar fashion to how the GET request works ... I expected 
> something like this
> [{'vcf_string':' ... ', 'input':'NM_..'}
> {'warning':' ... ', 'input':'NM_..'}]
>
> i.e. each list item would correspond to one input value .. and each 
> dictionary would be populated with the resultant 'vcf_string' .. or 
> 'warning' .. if the HGVS input is malformed.
>
> However, the output does not appear to be consistent.
>
> Example 1:
>
> For input values, "NM_000070.2:c.?", "NM_000070.2:c.328C>T", there 
> appears to be only one list item
> {'vcf_string': ['15-42676699-C-A', '15-42676699-C-T'], 'warnings': 
> ["No variant found with ID 'NM_000070.2:c.?'"], 'input': 
> 'NM_000070.2:c.328C>T'}
>
> This erroneously (I think) mixes the warning from the first input 
> value and the translated vcf coordinates from the second input value
>
> Example 2:
>
> Some HGVS coordinates that are valid and are properly converted via 
> the GET request, are not handled here:
> e.g. "No variant found with ID 'NM_000070.2:c.545T>A'"
>
> *Code*
>
> import requests, sys
>
> server = "https://grch37.rest.ensembl.org"
> ext = "/variant_recoder/homo_sapiens"
> headers={ "Content-Type" : "application/json", "Accept" : 
> "application/json"}
> params={"fields":"vcf_string"}
> hgvs_ids='{"ids": ["NM_000070.2:c.?", "NM_000070.2:c.328C>T", 
> "NM_000070.2:c.545T>A", "NM_000070.2:c.701G>A", 
> "NM_000070.2:c.1838del", "NM_000070.2:c.945+1del", 
> "NM_000070.2:c.1061T>G", "NM_000070.2:c.1079G>A", 
> "NM_000070.2:c.1342C>G", "NM_000070.2:c.1468C>T", 
> "NM_000070.2:c.550delA?", "NM_000070.2:c.550del", 
> "NM_000070.2:c.1715G>A", "NM_000070.2:c.2069_2070del", 
> "NM_000070.2:c.2306G>A", "NM_000070.2:c.2314_2317del", 
> "NM_000070.2:c.2362_2363delinsTCATCT", "NM_000070.2:c.946-1G>A", 
> "NM_000070.2:c.1466G>A", "NM_000070.2:c.2230A>G", 
> "NM_000070.2:c.19_23del", "NM_000070.2:c.257C>T", 
> "NM_000070.2:c.402del", "NM_000070.2:c.1913A>C", 
> "NM_000070.2:c.1622G>A", "NM_000070.2:c.598_612del", 
> "NM_000070.2:c.801+1G>A", "NM_000070.2:c.664G>A", 
> "NM_000070.2:c.2243G>A", "NM_000070.2:c.717del"]}'
>
> r = requests.post(server+ext, headers=headers, data=hgvs_ids, 
> params=params)
>
> if not r.ok:
>   r.raise_for_status()
>
> decoded = r.json()
> print(repr(decoded))*
> *
>
> *Results*
>
> [{'vcf_string': ['15-42676699-C-A', '15-42676699-C-T'], 'warnings': ["No variant found with ID 'NM_000070.2:c.?'"], 'input': 'NM_000070.2:c.328C>T'}, {'input': 'NM_000070.2:c.701G>A', 'warnings': ["No variant found with ID 'NM_000070.2:c.545T>A'"], 'vcf_string': ['15-42681194-G-A']}, {'vcf_string': ['15-42700445-AA-A'], 'input': 'NM_000070.2:c.1838del'}, {'input': 'NM_000070.2:c.1061T>G', 'warnings': ["No variant found with ID 'NM_000070.2:c.945+1del'"], 'vcf_string': ['15-42686485-T-G']}, {'vcf_string': ['15-42686503-G-A'], 'input': 'NM_000070.2:c.1079G>A'}, {'vcf_string': ['15-42691838-C-G', '15-42691838-C-T'], 'input': 'NM_000070.2:c.1342C>G'}, {'input': 'NM_000070.2:c.1468C>T', 'vcf_string': ['15-42693952-C-T']}, {'input': 'NM_000070.2:c.550del', 'vcf_string': ['15-42680001-AA-A'], 'warnings': ["No variant found with ID 'NM_000070.2:c.550delA?'"]}, {'input': 'NM_000070.2:c.1715G>A', 'vcf_string': ['15-42695170-G-A', '15-42695170-G-C', '15-42695170-G-T']}, {'vcf_string': ['15-42703124-G-A', '15-42703124-G-C'], 'warnings': ["No variant found with ID 'NM_000070.2:c.2069_2070del'"], 'input': 'NM_000070.2:c.2306G>A'}, {'input': 'NM_000070.2:c.2314_2317del', 'vcf_string': ['15-42703130-CAGAC-C']}, {'vcf_string': ['15-42703179-TAG-TTCATCT'], 'input': 'NM_000070.2:c.2362_2363delinsTCATCT'}, {'warnings': ["No variant found with ID 'NM_000070.2:c.946-1G>A'"], 'vcf_string': ['15-42693950-G-A'], 'input': 'NM_000070.2:c.1466G>A'}, {'input': 'NM_000070.2:c.2230A>G', 'vcf_string': ['15-42702831-A-G']}, {'warnings': ["No variant found with ID 'NM_000070.2:c.19_23del'"], 'vcf_string': ['15-42652260-C-T'], 'input': 'NM_000070.2:c.257C>T'}, {'vcf_string': ['15-42678386-CC-C'], 'input': 'NM_000070.2:c.402del'}, {'vcf_string': ['15-42695077-G-A'], 'warnings': ["No variant found with ID 'NM_000070.2:c.1913A>C'"], 'input': 'NM_000070.2:c.1622G>A'}, {'vcf_string': ['15-42680049-GTTCTGGAGTGCTCTG-G'], 'input': 'NM_000070.2:c.598_612del'}, {'vcf_string': ['15-42681157-G-A'], 'warnings': ["No variant found with ID 'NM_000070.2:c.801+1G>A'"], 'input': 'NM_000070.2:c.664G>A'}, {'input': 'NM_000070.2:c.2243G>A', 'vcf_string': ['15-42702844-G-A']}, {'vcf_string': ['15-42681205-TT-T', '15-42681205-TT-TTT'], 'input': 'NM_000070.2:c.717del'}]
> Thanks,
> Josh
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