Issue #18. Add pre-computed outputs for the valid files

[PeterKnealeCMRI]

Added basic logic to pre-translate the valid HGVS entries.
I've left it running on my machine to translate the rest, will take 1-2 hours.

HGVS,Chromosome,Position,Ref,Alt
NM_001110556.2:c.3396G>T,X,154360399,C,A
NM_000284.4:c.1172_*3del,X,19359651,TAAGGG,T
NM_004006.3:c.8547+18C>T,X,31496770,G,A
NM_172245.4:c.780+135G>A,Y,1294596,G,A
NM_001353921.2:c.145A>G,X,63724597,T,C

[h-joshi]

I just realised, some genes have duplicates in both chromosome X and Y

## Request (2)
curl -X "POST" "https://rest.ensembl.org/variant_recoder/homo_sapiens?fields=None&vcf_string=1" \
     -H 'Content-Type: application/json' \
     -H 'Accept: application/json' \
     -d $'{
  "ids": [
    "NM_172245.4:c.780+135G>A",
    "NM_006883.2:c.*5G>A",
    "NM_000451.4:c.106C>T",
    "NM_172245.4:c.663C>A",
    "NM_000451.4:c.49A>T",
    "NM_172245.4:c.960G>C",
    "NM_006883.2:c.-432-45C>T",
    "NM_000451.4:c.506G>A",
    "NM_172245.4:c.855C>T",
    "NM_000451.4:c.391G>T",
    "NM_172245.4:c.473+12C>T",
    "NM_000451.4:c.463G>T",
    "NM_172245.4:c.132G>T",
    "NM_000451.4:c.583C>T",
    "NM_000451.4:c.633+5C>G",
    "NM_172245.4:c.220-80G>A",
    "NM_172245.4:c.947-14G>A"
  ]
}'

For entries in output.csv, where the chromosome is "Y", it is Ok to replace the chromosome with "X". All of these genes have paralogs (duplicate genes) that have identical chromosome coordinates irrespective of whether it's X or Y (output pasted below)

As a side, Modify the download.py script, so that only the entry beginning with X- is picked up as the translated VCF

[
  {
    "A": {
      "input": "NM_172245.4:c.780+135G>A",
      "vcf_string": [
        "Y-1294596-G-A",
        "LRG_186-30797-G-A",
        "X-1294596-G-A"
      ]
    }
  },
  {
    "A": {
      "input": "NM_006883.2:c.*5G>A",
      "vcf_string": [
        "Y-658834-G-A",
        "X-658834-G-A",
        "LRG_710-39491-G-A"
      ]
    }
  },
  {
    "T": {
      "vcf_string": [
        "Y-631003-C-T",
        "X-631003-C-T",
        "LRG_710-11660-C-T"
      ],
      "input": "NM_000451.4:c.106C>T"
    }
  },
  {
    "A": {
      "input": "NM_172245.4:c.663C>A",
      "vcf_string": [
        "Y-1294344-C-A",
        "LRG_186-30545-C-A",
        "X-1294344-C-A"
      ]
    }
  },
  {
    "T": {
      "vcf_string": [
        "Y-630946-A-T",
        "X-630946-A-T",
        "LRG_710-11603-A-T"
      ],
      "input": "NM_000451.4:c.49A>T"
    }
  },
  {
    "C": {
      "input": "NM_172245.4:c.960G>C",
      "vcf_string": [
        "Y-1303936-G-C",
        "LRG_186-40137-G-C",
        "X-1303936-G-C"
      ]
    }
  },
  {
    "T": {
      "vcf_string": [
        "Y-630421-C-T",
        "X-630421-C-T",
        "LRG_710-11078-C-T"
      ],
      "input": "NM_006883.2:c.-432-45C>T"
    }
  },
  {
    "A": {
      "input": "NM_000451.4:c.506G>A",
      "vcf_string": [
        "Y-640840-G-A",
        "X-640840-G-A",
        "LRG_710-21497-G-A"
      ]
    }
  },
  {
    "T": {
      "input": "NM_172245.4:c.855C>T",
      "vcf_string": [
        "Y-1300535-C-T",
        "LRG_186-36736-C-T",
        "X-1300535-C-T"
      ]
    }
  },
  {
    "T": {
      "input": "NM_000451.4:c.391G>T",
      "vcf_string": [
        "Y-634731-G-T",
        "X-634731-G-T",
        "LRG_710-15388-G-T"
      ]
    }
  },
  {
    "T": {
      "vcf_string": [
        "Y-1288900-C-T",
        "LRG_186-25101-C-T",
        "X-1288900-C-T"
      ],
      "input": "NM_172245.4:c.473+12C>T"
    }
  },
  {
    "T": {
      "vcf_string": [
        "Y-634803-G-T",
        "X-634803-G-T",
        "LRG_710-15460-G-T"
      ],
      "input": "NM_000451.4:c.463G>T"
    }
  },
  {
    "T": {
      "input": "NM_172245.4:c.132G>T",
      "vcf_string": [
        "Y-1285833-G-T",
        "LRG_186-22034-G-T",
        "X-1285833-G-T"
      ]
    }
  },
  {
    "T": {
      "input": "NM_000451.4:c.583C>T",
      "vcf_string": [
        "Y-641037-C-T",
        "X-641037-C-T",
        "LRG_710-21694-C-T"
      ]
    }
  },
  {
    "G": {
      "vcf_string": [
        "Y-641092-C-G",
        "X-641092-C-G",
        "LRG_710-21749-C-G"
      ],
      "input": "NM_000451.4:c.633+5C>G"
    }
  },
  {
    "A": {
      "vcf_string": [
        "Y-1288439-G-A",
        "LRG_186-24640-G-A",
        "X-1288439-G-A"
      ],
      "input": "NM_172245.4:c.220-80G>A"
    }
  },
  {
    "A": {
      "vcf_string": [
        "Y-1303909-G-A",
        "LRG_186-40110-G-A",
        "X-1303909-G-A"
      ],
      "input": "NM_172245.4:c.947-14G>A"
    }
  }
]

[PeterKnealeCMRI]

Ok, I'm now filtering on those starting with X- as you can below with number 4, its skipping the Y- and LRG-

Progress 1/1954
        Examining X-154360399-C-A
                Accepted
Progress 2/1954
        Examining X-19359651-TAAGGG-T
                Accepted
Progress 3/1954
        Examining X-31496770-G-A
                Accepted
Progress 4/1954
        Examining Y-1294596-G-A
                Ignored
        Examining LRG_186-30797-G-A
                Ignored
        Examining X-1294596-G-A
                Accepted
Progress 5/1954
        Examining X-63724597-T-C
                Accepted