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CHANGELOG
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===============
Release History
===============
Version 2.1.0
==============
modisco
-------
- Make motif database-based reporting optional.
- Require Python 3.7.x to 3.10.x.
Version 2.0.7
==============
modisco
-------
- Adds an error if the window is larger than the sequences.
Version 2.0.6
==============
modisco
-------
- Adds an explicit casting of the one-hot encoded sequence and the
attributions to 32-bit floats. This allows files to be compressed to
16-bit floats to save space.
Version 2.0.5
==============
report.py
---------
- Removes the use of the Arial Rounded font, hopefully reducing the number
of warnings produced.
Version 2.0.4
==============
report.py
---------
- Removed the need to supply both a MEME file with motifs and a directory
with extracted PFMs. The PFMs will be read directly from the MEME file now.
modisco
-------
- Removed the need to supply both a MEME file with motifs and a directory
with extracted PFMs. The PFMs will be read directly from the MEME file now.
Version 2.0.3
==============
report.py
---------
- Fixed a minor error where results would not display properly if fewer
than the specified number of TOMTOM hits were found for a motif.
Version 2.0.2
==============
report.py
---------
- Fixed a display issue where the patterns were being displayed in the
wrong order.
Version 2.0.1
==============
Highlights
----------
- A minor bug and a minor convenience issue have been resolved.
aggregator.py
-------------
- A minor bug was fixed where, when collapsing patterns in the final step,
some patterns would have no seqlets after the filtering step and the code
would crash. Now, if a pattern has no seqlets after the filtering, it is
ignored.
report.py
---------
- The patterns are now displayed in numeric order 1-10, followed by 11-20,
etc., as opposed to by alphabetical order 1, 10-19, 2, 20-29, etc.
Version 2.0.0
==============
Highlights
----------
- This is the first complete release that includes breaking changes compared
with the original code. They are detailed below.
affinitymat.py
--------------
- When calculating the coarse-grained resolution, an argsort is done to find
the nearest neighbors of each seqlet. This is done in numpy using a sorting
algorithm that is not stable. This new version uses "mergesort" instead of
the default "quicksort", as it is a stable algorithm. This change allows
us to use numpy within numba, assigning more work to each thread, and
ultimately speeding the code up ~2-3x.
core.py
-------
- AggregatedSeqlet was renamed SeqletSet.
gapped_kmer.py
--------------
- A bug in the original codebase where the nucleotide identity was done
on the argmax of the contribution score, rather than the one-hot encoded
sequence, caused incorrect nucleotide calls for positions that had a
negative contribution. This effects only the gapped k-mer representation
used to calculate coarse-grained representations, not the found patterns.
io.py
-----
- This code was added to handle saving the outputs of the TFMoDISco function
to disk and the conversion of the old outputs into the new format.
tfmodisco.py
------------
- The output of TFMoDISco is now a tuple of two lists, where the first
list contains the positive patterns and the second list contains the
negative patterns. Each pattern is represented as a `SeqletSet` object.
Version 1.0.0
==============
Highlights
----------
- This is the first complete release that perfectly reproduces the outputs
of the original TF-MoDISco code.