{"action":"opened","issue":{"url":"https://api.github.com/repos/hammerlab/pyensembl/issues/112","labels_url":"https://api.github.com/repos/hammerlab/pyensembl/issues/112/labels{/name}","comments_url":"https://api.github.com/repos/hammerlab/pyensembl/issues/112/comments","events_url":"https://api.github.com/repos/hammerlab/pyensembl/issues/112/events","html_url":"https://github.com/hammerlab/pyensembl/issues/112","id":98835690,"number":112,"title":"Load mouse VCF files","user":{"login":"iskandr","id":48441,"avatar_url":"https://avatars.githubusercontent.com/u/48441?v=3","gravatar_id":"","url":"https://api.github.com/users/iskandr","html_url":"https://github.com/iskandr","followers_url":"https://api.github.com/users/iskandr/followers","following_url":"https://api.github.com/users/iskandr/following{/other_user}","gists_url":"https://api.github.com/users/iskandr/gists{/gist_id}","starred_url":"https://api.github.com/users/iskandr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/iskandr/subscriptions","organizations_url":"https://api.github.com/users/iskandr/orgs","repos_url":"https://api.github.com/users/iskandr/repos","events_url":"https://api.github.com/users/iskandr/events{/privacy}","received_events_url":"https://api.github.com/users/iskandr/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-08-03T20:48:10Z","updated_at":"2015-08-03T20:48:10Z","closed_at":null,"body":"```\r\nIn [2]: varcode.load_vcf(\"mouse_vcf_dbsnp_chr1_partial.vcf\")\r\n---------------------------------------------------------------------------\r\nValueError                                Traceback (most recent call last)\r\n<ipython-input-2-2afb1e38979a> in <module>()\r\n----> 1 varcode.load_vcf(\"mouse_vcf_dbsnp_chr1_partial.vcf\")\r\n\r\n/Users/iskander/code/varcode/varcode/vcf.py in load_vcf(path, genome, only_passing, ensembl_version, reference_name, reference_vcf_key, allow_extended_nucleotides, max_variants)\r\n     99                 ensembl_version,\r\n    100                 reference_name,\r\n--> 101                 reference_vcf_key)\r\n    102\r\n    103         for record in handle.vcf_reader:\r\n\r\n/Users/iskander/code/varcode/varcode/vcf.py in make_ensembl(vcf_reader, ensembl_version, reference_name, reference_vcf_key)\r\n    483         else:\r\n    484             reference_path = vcf_reader.metadata[reference_vcf_key]\r\n--> 485             reference_name = infer_reference_name(reference_path)\r\n    486         ensembl_version = ensembl_release_number_for_reference_name(\r\n    487             reference_name)\r\n\r\n/Users/iskander/code/varcode/varcode/reference_name.py in infer_reference_name(path)\r\n     33\r\n     34     raise ValueError(\r\n---> 35         \"Failed to infer human genome assembly name for %s\" % path)\r\n     36\r\n     37 def ensembl_release_number_for_reference_name(name):\r\n\r\nValueError: Failed to infer human genome assembly name for GCF_000001635.22\r\n```\r\n\r\nSeems like this will require us downloading some correspondence table between assembly names (e.g. http://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi?REQUEST=SHOW_STATISTICS)"}}