Addresses issue #57. A GTF option has been included and now all gene...
Addresses issue #57. A GTF option has been included and now all gene information is extracted with the following hierarchy: GTF, gene_info table, biomaRT. It also uses the non-redundant exonic length (effective gene length) to calculate RPKMs and TPMs. If the GTF is not present it reverts to the old method. Tested with a planaria GTF, which does not contain gene names or any other information apart from ensembl_gene_id and transctipt_id. It might be good to test with a human / mouse GTF. TODO or at least to consider: (i) add GTF as a mandatory argument; (ii) use bioMart as a backup to find gene names and description if not present in the GTF (use case would some weird GTFs).
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