Offer support for conversion of gtf and gff files to MAVIS json format

[zhemingfan]

Overview

Currently, gtf and gff file formats are common file formats for storing information on annotations. As version 3 of MAVIS only supports json file formations for annotation, some level of support should be provided to users wanting to convert gtf and gff files into MAVIS accepted json files.

• [x] gtf file support
• [x] gff file support
• [x] Add unit tests that covers conversion of both types of formats

[creisle]

Seems like gtf/gff are the same

The GFF (General Feature Format) format consists of one line per feature, each containing 9 columns of data, plus optional track definition lines. The following documentation is based on the Version 2 specifications.

The GTF (General Transfer Format) is identical to GFF version 2.

-- https://m.ensembl.org/info/website/upload/gff.html

[creisle]

Looks like the latest version is GFF3 so maybe we should just support that? http://gmod.org/wiki/GFF3

@oneillkza What format are the gff files you have in? v3?

[oneillkza]

GTF

[oneillkza]

From Ensembl, so I guess GFF version 2.

[oneillkza]

But for sure it would make sense to also support GFF3

[creisle]

Added it as a tool for now, may include in the main package later on if it gets used a fair amount

[zhemingfan]

Based on internal testing, annotation file support is working as intended.