Version 0.18.0

[0.18.0] - 2023-01-11

Added

• gimme scan and gimme maelstrom now accept a random seed for (most) operations
  • for (optimal) deterministic behaviour, delete the cache and then run the command with a seed
• Scanner now accepts a np.random.RandomState and progress on init.
  • progress=None (the default) should print progress bars to the command line only, not to file.
• Scanner.set_genome now accepts the optional argument genomes_dir
• gimmemotifs.maelstrom.Moap.create now accepts a np.random.RandomState.
• gimmemotifs.maelstrom.run_maelstrom now accepts a np.random.RandomState.

Changed

• gimme diff (diff_plot() to be exact) will now print to stdout, like all other functions
• now using the logger instead of print/sys.stderr.write in many more places
• string formatting now (mostly) done with f-strings
• refactored Fasta class
• split scanner.py into 3 submodules:
  • scanner/__init__.py with the exported functions
  • scanner/base.py with the Scanner class
  • scanner/utils.py with the rest
• gimmemotifs/maelstrom.py renamed to gimmemotifs/maelstrom/_init__.py
  • rank.py and moap.py are now submodules of maelstrom.

Fixed

• gimme maelstrom works with or without xgboost (but will give a warning without xgboost)
• fixed warning "in validate_matrix(): Row sums in df are not close to 1. Reormalizing rows..."
• fixed multiprocess.Pool Warnings
• fixed a pandas copywarning (in gc_bin_bedfile() to be exact)
• fixed warnings when leaving files open
• fixed deprecation warning in maelstrom (and in tests)
• fixed futurewarning in report.py
• silence warnings from external tools in motif prediction (pp_predict_motifs() to be exact)
• updated last references from Motif.pwm_scan and Motif.pwm_scan_all to Motif.scan and Motif.scan_all respectively
• typo in gimme motifs output ("%matches background" to "% matches background")
• Scanner now uses a cheaper method to determine a genome's identity
  • (filesize + name instead of the md5sum of the whole genome's contents)
• gimme motifs gives an informative error when fraction is not within 0-1.
• gimme threshold works again

Removed

• removed old python2 code (scanning with MOODS & import shenanigans)

Version 0.17.2

[0.17.2] - 2022-10-12

Changed

• made xgboost an optional dependency (to save space on bioconda)
• an existing config will now update available tools when accessed (e4b3275)
• applied the bioconda patch to compile_externals.py (11b0c2c)
• coverage_table and combine_peaks have their positional arguments under positional arguments (20819ee)
• coverage_table should be slightly faster now (20819ee)

Fixed

• biofluff dependency back in requirements
• pinned conda and mamba versions in .travis.yaml
  • temp fix until conda>=4.12 can install mamba properly
• documentation is working again!
• gimmemotifs now supports pandas >=1.30

Removed

• pyarrow dependency

Version 0.17.1

Changelog

[0.17.1] - 2022-06-02

Fixed

• motifs require to have unique ids when clustering, thanks @akmorrow13!
• motif2factors removes apostrophes so it wont crash :)
• removed a print

Version 0.17.0

Changelog

[0.17.0] - 2021-12-22

Added

• Added --genomes_dir argument to gimme motif2factors.
• Added --version flag.
• Function sample() for fast sequence sampling from a Motif() instance.
• Added JASPAR 2022 motif databases.
• Updated Homer motif database.
• Operators:
  • + - take the combination of two motifs (average), based on pfm, which means that motifs with higher counts will be weighed more heavily.
  • & - take the combination of two motifs (average), based on the ppm, which means that both motifs will be weighed equally.
  • << - "shift" motif left (adding a non-informative position to the right side)
  • >> - "shift" motif right (adding a non-informative position to the left side)
  • ~ - reverse complement
  • * - multiply the pfm by a value
• Progress bar for scanning.
• list_installed_libraries() to list available motif libraries.

Changed

• Motif() class completely restructured:
  • Split into multiple files with coherent function.
  • Uses numpy.array internally.
  • All functions that mention pwm renamed to ppm (position-probability matrix), as the definition of a PWM is usually a log-odds matrix, not a probability matrix.
    • to_pwm() is deprecated, use to_ppm() instead.
  • Changed functions pwm_min_score() and pwm_max_score() to properties max_score and min_score.
  • All internal data is correctly updated when Motif() is changed, for instance by trimming (#218).

Fixed

• gimme motif2factors can now unzip genome fastas.
• gimme motif2factors will sanitize genome names.
• Fixed bugs related to partial rerun of gimme motif2factors.
• Fixed unhandled OSError during installation on Mac.
• Fixed bug related to RFE() (#226).
• Positional probability matrix now sum to 1 over all positions (#209).
• Fixed issue with pandas >= 1.3.
• Fixed issue with non_reducing_slice import from pandas.
• Fix threshold calculation if more than 20,000 sequences are supplied.
• Fix issue with config file getting corrupted.
• Fix FPR threshold calculation.

Version 0.16.1

[0.16.1] - 2021-06-28

Bugfix release.

Added

• Added warning when the number of sequences used for de novo motif prediction is low.

Fixed

• Fixed bug with gimme motif2factors.
• Fixed "Motif does not occur in motif database when running maelstrom" (#192).
• Fixed bugs related to runs where no (significant) motifs is found.

Version 0.16.0

[0.16.0] - 2021-05-28

Many bugfixes, thanks to @kirbyziegler, @irzhegalova, @wangmhan, @ClarissaFeuersteinAkgoz and @fgualdr for reporting and proposing solutions!
Thanks to @Maarten-vd-Sande for the speed improvements.

Added

• gimme motif2factors command to annotate a motif database with TFs from different species
  based on orthogroups.
• Informative error message with link to fix when cache is corrupted (running on a cluster).
• Print an informative error message if the input file is not in the correct format.

Changed

• Speed improvements to motif scanning, which is now up to 2X faster!
• Size of input regions is now automatically adjusted (#123, #128, #129)
• Quantile normalization in coverage_table now uses multiple CPUs.

Fixed

• Fixes issue where % of motif occurence would be incorrectly reported in gimme maelstrom output (#162).
• Fix issues with running Trawler (#181)
• Fix issues with running YAMDA (#180)
• Fix issues with parsing XXmotif output (#178)
• Fix issue where command line argument (such as single strand) are ignored (#177)
• Fix pyarrow dependency (#176)
• The correct % of regions with motif is now reported (#162)
• Fix issue with running gimme motifs with the HOMER database (#135)
• Fix issue with the --size parameter in gimme motifs, which now works as expected (#128)

Version 0.15.3

[0.15.3] - 2021-02-01

Fixed

• _non_reducing_slice vs non_reducing_slice for pandas>=1.2 (#168)
• When using original region size, skip regions smaller than 10bp and warn if no
  regions are left.
• Fixed creating statistics report crashed with KeyError: 'Factor' (#170)
• Fixed bug with creating GC bins for a genome with unusual GC% (like Plasmodium).
• Fixed bug that occurs when upgrading pyarrow with an existing GimmeMotifs
  cache.

Version 0.15.2

[0.15.2] - 2020-11-26

Changed

• Refactoring to make coverage_table and combine_peaks available via API.

Fixed

• Fix issue with -s parameter of gimme motifs (#146)
• Fix issues (hopefully) with scanning large input files.

Version 0.15.1

[0.15.1] - 2020-10-07

Bugfix release.

Added

• Motif.plot_logo() accepts an ax argument.

Fixed

• Support for pandas>=1.1
• coverage_table doesn't add a newline at the end of the file.

Version 0.15.0

[0.15.0] - 2020-09-29

Added

• Added additional columns to gimme maelstrom output for better intepretation (correlation of motif to signal and % of regions with motif).
• Added support for multi-species input in genome@chrom:start-end format.
• gimme maelstrom warns if data is not row-centered and will center by default.
• gimme maelstrom selects a set of non-redundant (or less redundant) motifs by default.
• Added SVR regressor for gimme maelstrom.
• Added quantile normalization to coverage_table.

Removed

• Removed the lightning classifiers and regressors as the package is no longer actively maintained.

Changed

• Visually improved HTML output.
• Score of maelstrom is now an aggregate z-score based on combining z-scores from individual methods using Stouffer's method. The z-scores of individual methods are generated using the inverse normal transform.
• Reorganized some classes and functions.

Fixed

• Fixed minor issues with sorting columns in HTML output.
• gimme motifs doesn't crash when no motifs are found.
• Fixed error with Ensembl chromosome names in combine_peaks.