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CHANGELOG.rst

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Change Log

2.6.12

  • Parse fastq-dump version 3.*

2.6.11

  • Fix parsing of fastq-dump version.

2.6.10

2.6.9

  • Pin pystan version to < 3.

2.6.8

  • Fix issue with parsing fastq-dump version.

2.6.7

  • Pin matplotlib, pandas, and plotnine versions to avoid errors, and stop testing barcodeInfoToCodonVariantTable as dms_variants has incompatible versions.

2.6.6

  • Ensure that dms2_batch_bcsubamp propagates --bclen / --bclen2 values of 0.

2.6.5

  • Fix bug in fastqFromSRA for newer versions of fastq-dump.
  • Specify pandas < 1.0

2.6.4

  • Added --bcinfo_csv option to dms2_bcsubamp.

2.6.3

  • Edited syn_selection to add pseudocounts for odds ratio calculations in order to avoid null/inf values.

2.6.2

  • Added 'syn_selection'.

2.6.1

  • Added utils.codon_to_nt_counts.

2.6.0

  • Support python3.7 and pystan >= 2.19 and removed limit that scipy < 1.3.

2.5.1

  • Remove barcodes.fracIdentWithinBarcode as it is not correct. There is a new function being added in alignparse that calculates the empirical accuracy correctly.
  • Remove dependency on HTSeq.
  • Added --no_corr and --no_avg option to dms2_batch_prefs

2.5.0

  • Remove codonvarianttable module as it is now in dms_variants package
  • Remove neutcurve module as it is replated by neutcurve package
  • Parse - / + signs in PAF alignment scores.
  • Works with pandas 0.25

2.4.16

  • Added diffsel.beta_diversity

2.4.15

  • Relax dependency requirements for pysam

2.4.14

  • Allow non-integer --letterheight for dms2_logoplot

2.4.13

  • Added option for single-color logoplots for dms2_logoplot

2.4.12

  • Makes sample names a category to preserve order in plot.plotCodonMutTypes.

2.4.11

  • Adds functionality that can convert the *bc_info* files generated by dms2_bcsubamp into a CodonVariantTable.

2.4.10

  • Added mle method to findSigSel.

2.4.9

  • Allow multiprocessing fastqFromSRA
  • Updates to genotype-phenotype maps generated from CodonVariantTable func scores.

2.4.8

  • Allow bottleneck of None in simulateSampleCounts.
  • added CodonVariantTable.classifyVariants method
  • dms2_batch_bcsubamp handles --bcinfo argument

2.4.7

  • 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

  • Added function to create gpmap.GenotypePhenotypeMap from CodonVariantTable
  • Don't test rplot module, we now recommend dmslogo instead.
  • Work with version >=1.0 of umi_tools

2.4.5

  • 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

  • Fix to work with pandas 0.24 and newest regex

2.4.3

  • Bug fix to plotting mutation frequencies in CodonVariantTable

2.4.2

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

2.4.1

  • Moved CodonVariantTable class to its own module, codonvarianttable.

2.4.0

  • 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

  • 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

  • Improved appearance of histograms created by findSigSel
  • Fixed ymin for dms2_logoplot with small-valued fracsurvive

2.2.8

  • 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

2.2.6

  • 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

  • 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

  • added contour option to plot.plotCorrMatrix
  • added white_bg to plot.plotSiteDiffSel

2.2.3

  • added plot.findSigSel

2.2.2

  • added --bclen2 option to dms2_bcsubamp

2.2.1

  • 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

  • added compareprefs module
  • added rplot module to enable plotting with 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

  • 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

  • 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

  • A few packaging changes for PyPI

2.0.0

This version is a complete re-write of dms_tools version 1.2.2.