Arbitrary ROCs

What's new in 0.11.4

New Features

• You can now produce ROC and rolling AUC-ROC graphs compared against arbitrary folded sections using --struct-sect {section}. Previously, if you didn't provide an explicit CT file, you were obligated to use the folded section that was the same as the section from which the data came.
• The option for the explicit CT file has been renamed from --structs to --struct-file.

Full Changelog: v0.11.3...v0.11.4

Deep Pool

What's new in 0.11.3

Deep pooling

• You can now use seismic pool to pool together samples that are themselves pooled. The original samples will be deduplicated if they appear in multiple pooled samples.

Full Changelog: v0.11.2...v0.11.3

Fold/Export Pooled Samples

What's new in 0.11.2

Bug Fixes

• Fixed bug where Fold and Export steps crashed with pooled samples (non-pooled samples still ran successfully).

Full Changelog: v0.11.1...v0.11.2

Non-Redundant Window Info

What's new in 0.11.1

Bug fixes

• Fixed a minor bug where the window size and minimum data appeared twice in file names of rolling correlation/comparison graphs from seismic graph corroll.

Full Changelog: v0.11.0...v0.11.1

Pooled Samples

What's new in 0.11.0

New Features

• New command seismic pool allows you to pool samples after seismic relate. The archetypal use case would be if you have two or more replicate samples and you want to pool them to treat them as one sample.

Documentation

• Documentation has been updated to include seismic pool.

API Internals

• seismicrna.core.data has been largely rewritten to accommodate pooled datasets.

Full Changelog: v0.10.0...v0.11.0

v0.10.0

What's new in 0.10.0?

Features

• Five new types of graphs:

  • histpos: histogram of mutations per position
  • histread: histogram of mutations per read
  • roc: receiver operating characteristic (ROC)
  • aucroll: rolling area under the curve of ROC
  • corroll: rolling correlation/comparison between profiles

• Graphs seqbar and diffbar were renamed to profile and delprof, respectively.

• Graphs that compare pairs of tables (corroll, delprof, and scatter) can now compare all combinations of 2 tables from a list (with --comppair) as well as compare each table to itself (with --compself).

Documentation

• Documentation for how to use the main workflow is now up to date.

What's Changed

• 0.10.0 by @matthewfallan in #9

Full Changelog: v0.9.8...v0.10.0

VARNA Floats

What's new in 0.9.8?

Bugfixes

• Fixed bug where VARNA color values would be output in scientific notation instead of plain decimal notation, causing some programs to fail when parsing them.

Full Changelog: v0.9.7...v0.9.8

Improve Include G/U

What's new in v0.9.7

Bug fixes

• Patched bug where --include-gu would make SEISMIC-RNA crash. Credit to @justinaruda.

Documentation

• Add Justin Aruda (@justinaruda) to list of authors.

What's Changed

• 0.9.6 by @matthewfallan in #8

Full Changelog: v0.9.6...v0.9.7

Export All Positions

What's new in v0.9.6

Features

• New option --all-pos/unmasked-pos in seismic export web enables toggling between exporting only unmasked positions (default, and the only option in v0.9.5) and all positions.

Full Changelog: v0.9.5...v0.9.6

Mask Efficiently

What's new in v0.9.5

Performance

• The function apply_mask has been made more efficient in the common case that most of the reads are kept. Credit to @justinaruda.

Documentation

• Documentation for the main workflow has been updated.

What's Changed

• Optimized masking by replacing np.intersect1d() with np.setdiff1d(). by @justinaruda in #5
• Improved np.setdiff1d() logic during masking. by @justinaruda in #6
• 0.9.5 by @matthewfallan in #7

Full Changelog: v0.9.4...v0.9.5