Fix issues in "make_one_canonical_transcript_per_gene.py" script

[pieterlukasse]

Ticket to make sure the issues found and discussed in #58 comment are investigated and fixed. Main suspect is the following script:

• https://github.com/genome-nexus/genome-nexus-importer/blob/master/scripts/make_one_canonical_transcript_per_gene.py

[leexgh]

For the question: "some genes do not have a value in ensembl_canonical_gene, but do have ensembl transcript ids set for mskcc_canonical_transcript and uniprot_canonical_transcript", for example gene "GAGE5"

• ensembl_canonical_gene doesn't have value because it tries to find a match from ensembl_biomart_geneids by gene_stable_id or hgnc_symbol. But ensembl_biomart_geneids doesn't contain this gene so it has no value.
• mskcc_canonical_transcript and uniprot_canonical_transcript has value because it ties to find a match from overrides tables by hgnc_symbol, which are isoform_overrides_at_mskcc_grch38 and isoform_overrides_uniprot, but the overrides table contains those genes so they are able to find a match and put in a value