Simplify annotation to dictionary construction

[nadiadavidson]

Current code is:

Convert dataframes to GRanges object

tx_grangesList <- blessy.dfToGRangesList(tx_df)
domain_grangesList <- blessy.dfToGRangesList(domain_df)

Map domains to transcripts

mapped_df <- blessy.mapDomainToTranscript(tx_grangesList, domain_grangesList, tx_df, domain_df)

It would be good to have a mapDomainToTranscript function that just takes the output from the UCSC tracks function and does the Granges coversion automatically. ie:

mapped_df <- blessy.mapDomainToTranscript(tx_df, domain_df)

The function:
mapped_df <- blessy.mapDomainToTranscript(tx_grangesList, domain_grangesList, tx_df, domain_df)
Is also a little odd in that it's taking the same information twice (ie. tx_df and tx_grangesList). Could it not just be:
mapped_df <- blessy.mapDomainToTranscript(tx_grangesList, domain_grangesList)?

[nadiadavidson]

Following on from this and reading a little further into the documentation, I think what would be best are some methods that automate the whole dictionary creation starting with the annotations (as either a track name, a bed-like table or Granges file). ie.

blessy.createPhasingDictionary(genome,trans_track_name, domain_track_name)
blessy.createPhasingDictionary(tx_df, domain_df)
blessy.createPhasingDictionary(tx_grangesList, domain_grangesList)