can load PacBio transcripts and exons from LRP pipeline output
PacBioTranscript has SQANTI classification (FSM, ISM, NIC, NNC) as an attribute
PacBioTranscript and GencodeTranscript have a new many-to-one relationship indicating association between FSM/ISM transcripts and the reference transcript they match
ExceptionLogger helper class for reporting exceptions w/o halting entire script
IsoformPlot changes:
updated color schemes for different transcript types and pblock categories
isoform information can now be displayed in a table to the left of the plot
IsoformPlot can be drawn inside a subplot
refactoring:
ORF objects are now constructed from CDS intervals in gtf file instead of transcript-relative intervals in fasta headers
database loads from GENCODE comprehensive set
database only loads genes designated protein_coding
initialization of attributes in Protein class moved out of reconstructor methods and into cached properties
additions:
refactoring:
protein_codingcloses #71, #74