0.5.0 roadmap

[gfudenberg]

interval operations

• sort_bedframe default w/o view added natsort option to ops.sort_bedframe #86

io

• move encode client to sandbox, move parquet to sandbox
• delete read_ucsc_mrnafile
• sandbox parse_gtf_attributes().
• add docstrings for: read_tabix, read_pairix, read_bam, etc.
• develop tutorial for fetchers, fileops, & io
• refactor read_gapfile into fetch_centromeres
• tests for io

Tutorials and Docs

• add a 'how do I' for finding strand-specific upstream/downstream genomic features

Data

• populate the data folder with chromsizes for yeast, celegans, mouse, drosophila, ...

Future

• behavior of on=[] #91
  • add on=[] option for subtract, complement.
  • add on=[] for closest(). challenge is that filtering is done inside the function. consider passing a user-defined filtering function. This could replace ignore_upstream, ignore_overlaps flags.
• consider replacing the repeated get_default_colnames() and _verify_columns() in each ops with either a decorator or a function that does both.

io

• either refactor parse_gtf_attributes as read_gtf() with an option to parse, or wrap an existing tool for gtf parsing into a pandas dataframe.

• new frontend function for locally stored genome assemblies Local sources of truth for common genome assembly metadata #107

  • tutorial entry
  • change default for filter_chroms
  • add a test for the data (e.g. download from original site and check that names & lengths match)

• allow extract_centromeres to accept a path to a file

• io.to_bed function to save bedframe into bed (incl. resorting columns, dropping those not compatible with the bed format, and formatting the comment line) io.to_bed() #72

bin ops

• bin-table operations #116
• definitions
• functions
  • regions_to_bins to assign binspans to a set of bp spans
  • align_tables Find a way to ensure alignment of two interval tables. #37

Tutorials and Docs

• add tutorial for finding strand-specific upstream/downstream genomic features

[nvictus]

Closing in favor of project