Changelogs » Dms-tools2

Dms-tools2

2.4.10

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* Added `mle` method to `findSigSel`.

2.4.9

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* Allow multiprocessing `fastqFromSRA`

* Updates to genotype-phenotype maps generated from `CodonVariantTable` func scores.

2.4.8

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* Allow bottleneck of `None` in `simulateSampleCounts`.

* added `CodonVariantTable.classifyVariants` method

* `dms2_batch_bcsubamp` handles `--bcinfo` argument

2.4.7

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* Added `CodonVariantTable.from_simulation` method.

* Handle large facet plots in ``dms2_batch_bcsubamp`` & ``plotSiteDiffSel``

* Correctly handle missing output for individual samples in ``dms2_batch_*`` programs.

2.4.6

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* Added function to create `gpmap.GenotypePhenotypeMap` from `CodonVariantTable`

* Don't test `rplot` module, we now recommend `dmslogo <https://jbloomlab.github.io/dmslogo/>`_ instead.

* Work with version >=1.0 of `umi_tools`

2.4.5

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* Handle single sample groups in `dms2_batch_diffsel` and `dms2_batch_fracsurvive`

* added `utils.sigFigStr`

* make compatible with latest `natsorted`

* added `diffsel.df_read_filecols`

2.4.4

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* Fix to work with pandas 0.24 and newest regex

2.4.3

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* Bug fix to plotting mutation frequencies in `CodonVariantTable`

2.4.2

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* Enhancements to `codonvarianttable`, including simulating data with simulated latent / global phenotypes, and more plotting.

2.4.1

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* Moved `CodonVariantTable` class to its own module, `codonvarianttable`.

2.4.0

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* added `muteffects` data type to ``dms2_logoplot``

* added `highlighted_sites` option to `plot.plotSiteDiffSel`

* added `title` to `siteSubsetGGSeqLogo`

* Improve matching of termini tags when there are mismatches in `dms_tools2.pacbio`

* Some updates to `dms_tools2.minimap2.Mutations` objects.

* Added functionality to `dms_tools2.barcodes` to get identity within barcodes, take consensus of sequences with same barcode, and then use barcoded codon variants to call mutations.

* `pacbio.CCS` handles FASTQ as well as BAM input.

2.3.0

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* Require Python 3.6 or greater.

* added `pacbio`, `minimap2`, and `seqnumbering` modules.

* ``import dms_tools2`` now imports all non-optional modules in the package

2.2.9

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* Improved appearance of histograms created by `findSigSel`

* Fixed ymin for `dms2_logoplot` with small-valued fracsurvive

2.2.8

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* Cleaned up organization of examples and added `Dingens2018` and `Lee2018`.

* Fix setting of `matplotlib` backend, which was causing errors.

* Use loose versions in `sra`.

2.2.7

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* Make `diffsel` and `fracsurvive` compatible with `this pandas 0.23 update <https://pandas.pydata.org/pandas-docs/stable/whatsnew.htmlassign-accepts-dependent-arguments>`_

2.2.6

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* fix bug in `diffsel.tidyToWide` such that sites with matching values (i.e. all 0 values) are not dropped during de-duplication.

* added `utils.codonEvolAccessibility` function

2.2.5

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* fix bug in stringency re-scaling by ``dms2_logoplot``

* fix bug in axis scaling in `plot.plotCumulMutCounts`

* added `Haddox2018` and `Doud2018` examples and doc links

2.2.4

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* added `contour` option to `plot.plotCorrMatrix`

* added `white_bg` to `plot.plotSiteDiffSel`

2.2.3

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* added `plot.findSigSel`

2.2.2

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* added `--bclen2` option to ``dms2_bcsubamp``

2.2.1

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* added `protstruct` module for operations related to protein structurs

* added `neutcurve` module to fit neutralization curves

* updated required versions of some dependencies

2.2.0

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* added `compareprefs` module

* added `rplot` module to enable plotting with `ggseqlogo <https://omarwagih.github.io/ggseqlogo/>`_

* Added `omega` overlay option to ``dms2_logoplot``

* Fix bug with ``dms2_logoplot`` when using wildtype sequence overlays

* Fix bug with ``--fracsurvivemax 0`` to ``dms2_logoplot``

* Scale pseudocounts when using ``dms2_prefs`` with ``--method ratio``, which should give more accurate values when depths differ across samples.

* Some minor bug fixes.

* Fix bug with handling of disulfide-bonded cysteines in ``dssp`` output.

* Added `colors` option to `plot.plotCorrMatrix`

* Added ``--diffprefs`` option to ``dms2_logoplot``

2.1.0

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* Added programs and docs for `fracsurvive`.

* Added ``--scalebar`` to ``dms2_logoplot``.

* Add `grouplabel` option and preserve group order for faceted plots by batch programs.

* Handle dependencies without `__version__` attribute

2.0.2

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* Added ``--sitemask`` option to ``dms2_bcsubamp`` / ``dms2_batch_bcsubamp``.

* Standardized color scheme in ``*_cumulmutcounts.pdf`` plot.

* Ensure naturally sorted average prefs from ``dms2_batch_prefs``.

2.0.1

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* A few packaging changes for PyPI

2.0.0

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This version is a complete re-write of `dms_tools <https://github.com/jbloomlab/dms_tools>`_ version 1.2.2.