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MontgomeryLab / tinyRNA

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.
GNU General Public License v3.0
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tiny-count: adding classifier support to sequence-based counting #287

Closed AlexTate closed 1 year ago

AlexTate commented 1 year ago

Counts for individual reference sequences are subset by Classify as... values in sequence-based counting mode. Unit tests have been added for the ReferenceSeqs class.

In unit_tests_hts_parsing.py, I split up the gigantic test suite by target class. This is a good thing but it makes the diff wildly out of control on this PR because I didn't commit the reorganization before adding the ReferenceSeqsTests class.

Additionally, both GFFValidator and SamSqValidator classes now report when validation has finished

Closes #277

taimontgomery commented 1 year ago

Reviewed documentation. Tested on ram1 data.