Initial development

[RSWilson1]

This is a script which parses a gff file (refseq) and a tsv containing HGNC_ids and associated annotation. Using this it produced a bed file which is collapses of all the transcripts which match the HGNC ids and an igv html report of the bed file for viewing.

• Uses gff2pandas.py which has been modified to work with dtypes.
• igv_report.py is used for calling create_report from igv_reports to create the the html report of the bed file.
• gene_annotation2bed.py in the main script to run containing the required functions to extract the relevant transcripts and merge overlapping regions in the bed file.

Still to develop:

• Adding columns to html report by using a tsv file + add bed file as additional track with track config.
• Add more tests particularly for edge cases.
• Add handling of transcripts as input.
• Creating a vcf for testing with VEP.

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This change is 

[RSWilson1]

Additional to do: Write Readme explaining the scripts and requirements.txt.