gimmemotifs - 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)

- Python
Published by siebrenf about 3 years ago

gimmemotifs - 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

- Python
Published by siebrenf over 3 years ago

gimmemotifs - 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

- Python
Published by Maarten-vd-Sande almost 4 years ago

gimmemotifs - 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.

- Python
Published by simonvh about 4 years ago

gimmemotifs - 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.

- Python
Published by simonvh over 4 years ago

gimmemotifs - 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)

- Python
Published by simonvh almost 5 years ago

gimmemotifs - 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.

- Python
Published by simonvh about 5 years ago

gimmemotifs - 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.

- Python
Published by simonvh over 5 years ago

gimmemotifs - 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.

- Python
Published by simonvh over 5 years ago

gimmemotifs - 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.

- Python
Published by simonvh over 5 years ago

gimmemotifs - Release 0.14.4

[0.14.4] - 2020-04-02

Fixed

Fixed "TypeError: an integer is required (got type str)" when creating GC index.
Fixed combine_peaks with Ensembl chromosome names (thanks @JGAsmits).
Fixed bug with pandas>=1.0.

- Python
Published by simonvh almost 6 years ago

gimmemotifs - Release 0.14.3

Fixed

Fixed 'AttributeError: can't delete attribute' in gimme maelstrom and gimme motifs (#108, #109).

- Python
Published by simonvh about 6 years ago

gimmemotifs - Release 0.14.2

[0.14.2] - 2020-01-31

Bugfix release

Added

The combine_peaks script now supports .narrowPeak files.

Removed

Removed seqlogo dependency.
Removed obsolete code.

Changed

Refactored the tools section.

Fixed

Configuration issue with size instead of width (#103).
Updated tqdm requirement (#98).

- Python
Published by simonvh about 6 years ago

gimmemotifs - Version 0.14.1

- Python
Published by simonvh about 6 years ago

gimmemotifs - Version 0.14.0

Changelog

Added

The gimme motifs command supports new de novo motif prediction tools: DREME, ProSampler, YAMDA, DiNAMO and RPMCMC.
A set of non-redundant motifs is selected using recursive feature elimination for gimme motifs.
Motif scan results for non-redundant motifs are now included in the output.
Plot motif logos using different styles of visualization (information content, frequency, energy or Ensembl).
New scoring scheme that uses a z-score based on genomic sequences with a similar GC%.
CIS-BP motif database version 2.0 (Lambert et al. 2019).
JASPAR 2020 motif database.

Changed

Only three motif prediction tools are selected by default for gimme motifs: BioProspector, Homer and MEME.
The xl motif setting (motif width 6-20) is selected by default for gimme motifs.
Output names for files and reports of gimme motifs are now more consistent.
Command line tools gimme roc has been removed. This functionality has now been merged with gimme motifs. The gimme motifs command now scans for both known and de novo motifs.
Replaced weblogo/seqlogo with logomaker.
GC% background now uses a genomic index of GC% frequencies.
GC% z-score is now the default score for all gimme tools.

Fixed

FASTA files with > symbols in the header are now correctly parsed.
Fixed GC% background. The GC% background is now correct for all input formats.
factorial import for scipy >= 1.3.0.
All output columns in HTML reports can now be sorted correctly.

- Python
Published by simonvh about 6 years ago

gimmemotifs - Version 0.13.1

Added

Improved docstrings of several modules.
Added new API examples.

Fixed

The MEME motif tools should now be recognized after install.
Output of MEME 5.0.2 is now parsed correctly.
If the inputfile of gimme motifs is not recognized, a clear error message is printed.
Duplicate factors are removed from the motif factors list.

Changed

MEME is no longer included with GimmeMotifs. When installing via conda meme will be included. If GimmeMotifs is installed via pip, then MEME needs to be installed separately.
Changed "user" background to "custom" background.
Updated Posmo to run with a wider variety of settings.

- Python
Published by simonvh about 7 years ago

gimmemotifs - Version 0.13.0

Release 0.13.0 of GimmeMotifs.

[0.13.0] - 2018-11-19

Added

Multiple other motif databases (JASPAR, HOMER, HOCOMOCO, CIS-BP, ENCODE, Factorbook, SwissRegulon, IMAGE).
Helper script to combine peaks (summit files from MACS2)
Helper script to create coverage table (similar to bedtools multicov)
Option to report z-score normalized motif scores.
Added precision-recall AUC to stats and gimme roc.
gimme motifs now supports narrowPeak input.
Updated documentation with an explanation of the score that gimme maelstrom reports.

Changed

The maelstrom tools now use z-score normalized motif scores.
Improved efficiency of motif scanning (>10X speed improvement).
Removed dependency on R for rank aggregation.
Dropped support for Python 2.
Use versioneer for versioning.
Removed the default genome in config file.
Config file is now independent from GimmeMotifs version and will be created by default on first use.
Simplified setup.py script.
Updated parameters for ChIPMunk motif finder.

Fixed

Fixed the seqcor similarity metric to use a non-random sequence and to also take the reverse complement of motif 2 into account.
Improved the speed of gimme roc.
Fixed memory leak of gimme roc.
Fixed scale for newer pandas/sklearn combo
FIxed bug related to backgroundgradient with new pandas

- Python
Published by simonvh over 7 years ago

gimmemotifs - Version 0.12.0

I am happy to announce GimmeMotifs version 0.12.0.

Notable changes

You can specify the number of threads to use on all command line tools
GimmeMotifs now uses the faidx index, which means that gimme index is no longer necessary. This also means that you might have to reinstall your genomes.

See further changes here: CHANGELOG.md.

- Python
Published by simonvh over 7 years ago

gimmemotifs - Version 0.11.1

Bugfix release

Fixed issue with gimme genome
Fixed issue with gimme cluster
Fixed bug in gimme roc where html report would crash when no significant motif were found

- Python
Published by simonvh over 8 years ago

gimmemotifs - Version 0.11.0

Changelog:

Support for Python 3
Updated documentation
API for a lot of the functionality
New maelstrom command for differential motif analysis
Updated stats and graphical output for gimme roc
... and many more small changes

- Python
Published by simonvh over 8 years ago

gimmemotifs - Version 0.11.0-beta

Changelog:

Support for Python 3
Updated documentation
API for a lot of the functionality
New maelstrom command for differential motif analysis
Updated stats and graphical output for gimme roc
... and many more small changes

- Python
Published by simonvh over 8 years ago

gimmemotifs - Version 0.10.0

- Python
Published by simonvh almost 9 years ago

gimmemotifs - Version 0.10.0b6

- Python
Published by simonvh about 9 years ago

gimmemotifs - Version 0.10.0b5

- Python
Published by simonvh about 9 years ago

gimmemotifs - Version 0.10.0b4

- Python
Published by simonvh over 9 years ago

gimmemotifs - Version 0.10.0b3

Version 0.10.0b3

- Python
Published by simonvh over 9 years ago

gimmemotifs - Version 0.10.0b2

- Python
Published by simonvh over 9 years ago

gimmemotifs - Version 0.10.0b1

Version 0.10.0b1

- Python
Published by simonvh over 9 years ago