Exception handling for non-human species

[nakib103]

Description

• For non-human species some fields are not present in the VCF files, for example polyphen
• For non-human species primary source breaks

We need more exception handling in the code to handle these cases -

Check if index is valid -

ensembl-hypsipyle/common/file_model/variant.py

Line 325 in 63f2b39

csq_record_list[polyphen_index]

Try-except block does not work here (the code does not go to except block) -

ensembl-hypsipyle/common/file_model/variant.py

Line 32 in 63f2b39

try:

Example Query

query variant_example {
  variant(
    by_id: {genome_id: "c7335667-93e7-11ec-a39d-005056b38ce3", variant_id: "I:84:s01-84"}
  ) {
    name
    type
    slice {
      location {
        start
        end
      }
    }
    prediction_results {
      score
      result
      analysis_method {
        tool
        version
        qualifier
      }
    }
    allele_type {
      accession_id
      value
      url
    }
    alternative_names {
      name
    }
    alleles {
      name
    }
  }
}