tinyRNA provides an all-in-one solution for precision analysis of sRNA-seq data. At the core of tinyRNA is a highly flexible counting utility, tiny-count, that allows for hierarchical assignment of reads to features based on positional information, extent of feature overlap, 5’ nucleotide, length, and strandedness.
New synthetic sample data, reference data, and corresponding configuration files
TUTORIAL.md descriptions updated to indicate that the sample and reference data are synthetic. Removed link to the old WS279 dataset
Features Sheet column rename: Match -> Overlap
Updated Counter.md documentation
Updated Python scripts and unit tests
Documentation:
Descriptor updated in README.md and removed link to changelog.md
Removed changelog.md; moving forward changes will instead be detailed in major/minor release notes
Clarified PCA plot creation conditions
Updated helpstrings (mainly due to new ordering that places required arguments before optional arguments for Collapser and Counter. Plotter already did this)
Tests cleanup:
Removed unused datafiles: bowtie_indexes, WS279 gff, empty.sam, features.csv, unstranded.gff3, sample_sets, ls.yml, config.yml, paths.yml, run_config_template.yml. Configuration files are now pulled from the templates directory rather than maintaining a separate copy. For the vast majority of tests these files are being simulated anyway.
Removed unused scripts: create_test_data.py and memory_analysis.py
Updated unit tests
unit_tests_entry.py now prints captured exceptions. Previously they were being silently discarded which led to some confusion
Collapser:
Required arguments are now listed before optional arguments
Minor bugfix in the logic that determines whether trimming should take place. It would have never been triggered during normal operation but would if used as an import.
Counter:
Features that do not contain an Alias by... attribute key are no longer treated as an error; instead, these features will have an empty cell in the Feature Name column. This is in the spirit of reducing the user requirements for Counter.
Improved error handling in ReferenceTables
Required arguments are now listed before optional arguments
Clarified and corrected some comments
Plotter:
Now handles errors in the same way Counter does. The user is notified that they can use tiny replot rather than starting over.
The legend for sample_avg_scatter_by_dge has been moved back to where it is intended to be, within the plot space rather than to the right of the plot
tiny-deseq.r
Bugfix in the routine that restores the tagged multi-index that somehow snuck into the last PR
START_HERE directory:
Features Sheet column rename: Match -> Overlap
Documentation:
Tests cleanup:
Collapser:
Counter:
Alias by...attribute key are no longer treated as an error; instead, these features will have an empty cell in the Feature Name column. This is in the spirit of reducing the user requirements for Counter.Plotter:
tiny replotrather than starting over.tiny-deseq.r
Closes #2 (!)