CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.10.4] - 2025-1-2

Changed

• Changed filter-bam function into filter-file; Now accepts BED and CRAM in addition to BAM
• filter-file command can now accept a blacklist file

[0.10.3] - 2024-12-21

Fixed

• Update various docstrings and help statements to no longer mention SAM files as an accepted format

[0.10.2] - 2024-12-19

Fixed

• changed default args for wps would lead to errors. Now wps defaults to LWPS fragment lengths (120-180nt).

Changed

• made finaeltoolkit.utils.typing public. This is a module containing some useful type aliases
• minor formatting and typing changes
• renamed fraction_low and fraction_high to min_length and max_length for .utils.frag_array and .frag.wps. wps retains the deprecated arg names but issues a warning.

[0.10.1] - 2024-12-19

Fixed

• Added missing -n arg to end-motifs.
• Fixed incorrect ValueError regarding the negative_strand arg.
• Incorrect function name for wps leading to errors when called from CLI.

Added

• Additional tests for the CLI lazy loading implementation

[0.10.0] - 2024-12-18

Changed

• several modules containing implementations of fragmentomic features or utiliy functions have been made internal. This means there is now only one obvious import for each function. For example, multi_wps is imported from finaletoolkit.frag, and no longer can be imported from finaletoolkit.frag.multi_wps
• The CLI now uses lazy importing, drastically speeding up finaletoolkit when called from a command line.
• Added negative_strand option for end motifs related functions. When used in conjunction with both_strands, only end motifs on the negative (Crick) strand are considered in calculations.
• Renamed fraction_high and fraction_low in utils.utils.frag_generator to min_length and max_length.

Fixed

• deprecated arguments for end-motifs had default values which could lead to an error. This is fixed.

[0.9.1] - 2024-12-17

Fixed

• CLI no longer prints an error message if finaletoolkit is called without args.
• frag-length-bins, when writing a file, now writes the interval between min and max as inclusive. That is, previously when min=1 and max=2, only fragments of length 1 are reported. Now when such a result is calculated, the interval given is min=1 and max=1.
• Updated some descriptions and docstrings.

Added

• adjust-wps now has an option -S or --exclude-savgol to not perform Savitsky-Golay filtering.

Changed

• Several CLI options were renamed so that underscores become hyphens. This is for consistency and to simplify writing commands.

[0.9.0] - 2024-12-16

Removed

• strand_location arg from agg_bigwig
• cli_hist module

Fixed

• fixed bug involving tqdm progress bar in frag_length_intervals
• some code formatting
• fixed bug involving arg names in filter-bam
• add some missing args to CLI
• issues with running cleavage-profile (#115)
• issues with writing to bigwig with wps

Changed

• change default of arg both_strands of end_motifs to True to match behavior of original scripts
• rename fraction_high and fraction_low to min_length and max_length for all features, deprecating old args as aliases if needed.
• numpy 2 compatible
• fragmentomics functions assume Tabix indexed files all follow the FinaleDB Frag.gz file format. That is, columns are chrom, start, stop, score, and strand. If more columns are detect, a warning is issued, and FinaleToolkit will attempt to parse the file as a BED6 format.
• renamed genome_file to chrom_sizes for most functions.
• multi_wps and multi_cleavage_profile no longer return a value due to memory issues when attempting to calculate these genomewide. Instead, users should refer to the file specified with output_file.

Added

• internal utils._typing and utils._deprecation modules
• test for delfi

Deprecated

• delfi-gc-correct command. GC-correction is performed automatically by delfi already.

[0.8.0] - 2024-12-04

Removed

• finaletoolkit.frag.frag_length_bins no longer has the contig_by_contig option. This never had any functionality.
• finaletoolkit.frag.frag_length_bins no longer generates a text-based histogram.

Fixed

• contig_sizes option included for cleavage-profile CLI command.
• normalize option for coverage fixed so it no longer normalizes twice
• normalize=False for coverage runs much faster
• misc typehints and docstrings

Changed

• finaletoolkit.frag.frag_length_bins uses a dict based implementation that is more memory efficient.
• finaletoolkit.frag.frag_length_bins and finaletoolkit.frag.frag_length_intervals now take min_length and max_length keyword args to only consider fragments of certain lengths.
• flags for frag-length-bins and frag-length-intervals CLI commands updated to match Python API
• coverage default argument for normalize changed to False
• coverage default argument for scale_factor changed to 1.

Added

• finaletoolkit.frag.frag_length_bins can generate a histogram figure
• tests for frag_length module

[0.7.8] - 2024-11-28

Fixed

• update docs, docstring, and help message for wps to mention that site_bed must be sorted.

Added

• normalize keyword argument and --normalize flag to finaletoolkit.frag.coverage function and finaletoolkit coverage subcommand, respectively. Setting this argument/flag to true results in the output being normalized by the total coverage, ignoring scale_factor if specified.
• --intersect-policy or -p flag added to finaletoolkit coveragesubcommand.

[0.7.7] - 2024-11-27

Fixed

• subpackages can now be accessed when importing finaletoolkit. Previously, the following code resulted in an error:

>>> import finaletoolkit as ftk
>>> help(ftk.frag)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: module 'finaletoolkit' has no attribute 'frag'

Now this is a valid way to access subpackages cli, frag, genome, and utils.

[0.7.6] - 2024-11-18

Fixed

• indexing issue in region_end_motifs that would misread strand information when calculating end motifs on forward-strand only.

Changed

• frag_generator now accepts fragment coordinates in bed.gz files

[0.7.5] - 2024-10-10

Fixed

• delfi accepts gap_file=None
• update prog for delfi to reflect compatibility with reference genomes other than hg19

[0.7.4] - 2024-08-24

Changed

• Added many tests for util functions

Fixed

• Changed a nopython function to use numba compatible indexing

[0.7.3] - 2024-08-20

Changed

• Used "not" instead of "~" in an if statement
• Added a test for the coverage function

Fixed

• Ensured that the coverage value returns the expected value (previously returned an empty generator)

[0.7.2] - 2024-08-17

Changed

• Included output_file as required argument for finaletoolkit cleavage-profile.

Fixed

• Fixed incompatible types in min function through an explicit cast of chrom_sizes to integers.

[0.7.1] - 2024-08-11

Changed

• include chrom_sizes file as required argument for finaletoolkit cleavage-profile
• Numpy dependency version set to <2 to avoid breaking changes from numpy 2. This will change in the future as we migrate to use numpy 2.
• Replaced all instances of np.NaN with np.nan.

Fixed

• Fixed minor issues with typing in finaletoolkit.genome.gaps
• Fixed issue where data files are not packaged with FinaleToolkit

[0.7.0] - 2024-07-21

Added

• Brief description of modules in documentation under structure page
• Docstring
• finaletoolkit.version module containing single-source __version__ variable
• remove_nocov option in finaletoolkit.frag.delfi to toggle dropping two bins with low coverage. These bins are dropped in delfi_scripts but may not apply to fragment files not aligned to hg19.
• tests for finaletoolkit.frag.delfi_merge_bins

Changed

• finaletoolkit.frag.delfi changed to accept files aligned to almost any reference genome.
• finaletoolkit.frag.delfi_merge_bins algorithm changed to be reference genome-agnostic and consistent with delfi_scripts
• finaletoolkit delfi options -G, -M, and -R to drop gc-correction, merging, and remove nocov bins, respectively.

Removed

• unused flags for finaletools delfi: -W, --window-size
• redundant flags for finaletools delfi: -gc, --gc-correct, -m, --merge-bins

[0.6.5] - 2024-07-15

Changed

• utils.agg_bw now supports PathLike for input
• docstrings for frag.end_motifs.EndMotifsIntervals changed to be compatible with Sphinx

Fixed

• added missing gzip import for utils.agg_bw

Added

• tests for utils.agg_bw

[0.6.4] - 2024-06-04

Added

• interval_size argument for adjust_wps

Changed

• adjust_wps checks if median_window is larger than interval
• remove default options from some private helper functions for better error catching/predictable behavior.

Fixed

• wpsrelated functions and subcommands

[0.6.3] - 2024-05-31

Fixed

• fixed writing to bed.gz files when using coverage

[0.6.2] - 2024-05-30

Fixed

• adjusted handling of contig, start, stop for frag_generator so that coverage does not throw exceptions for genomewide intervals.

Added

• test for single_coverage

[0.6.1] - 2024-05-26

Changed

• add __version attribute
• finaletoolkit --version displays package version
• update PyPI page to include links

[0.6.0] - 2024-05-26

Fixed

• Fixed intersect policy for cleavage_profile. Now it calls frag_generator with a policy of any.
• Clean up some comments and docstrings
• Fixed logging from coverage function

Added

• Added numerous util functions
• Added left and right options to cleavage_profile and CLI cleavage-profile.
• Added tests for cleavage profile and WPS.

Changed

• Minimum Python version 3.9
• Changed filter_bam to have same filters as FinaleDB
• utils.frag_generator raises ValueError if start or stop are specified without contig
• Type hints changed to use literals when possible

Removed

• Removed utils.get_contig_lengths
• Removed data, conda_envs, and figs directories
• Removed unused dependencies click, pybedtools, and `cython
• Remove some unused imports from module files

[0.5.2] - 2024-05-08

Fixed

• interval-mds CLI subcommand calculates correctly without large negative values.
• interval-mds CLI subcommand now correctly parses tsv files.

Added

• Most end-motif related Python functions accept Path instances as inputs for files.
• Unit and function tests, especially for end-motif related functions.

[0.5.1] - 2024-05-03

Changed

• All instances of finaletools have been renamed to finaletoolkit
• All default tabular files are now TSV
• Update contacts in TOML

Fixed

• interval-mds and mds both calculate correctly when one motif has a frequency of 0

[0.5.0] - 2024-04-24

Added

• Added finaletools.interval_end_motifs function to calculate end-motifs over genomic intervals. Stores results in an IntervalEndMotifs object.
• Added CLI subcommand interval-end-motifs to calculate end-motifs over genomic intervals.
• Added CLI subcommand interval-mds to calculate MDS over intervals from interval end-motifs table.

Changed

• Added gc_correct option to delfi_merge_bins so that merging is possible without GC correction

Fixed

• delfi can now be run with gc_correct=false and merge_bins=true
• fixed cleavage_profile import in frag

[0.4.5] - 2024-04-9

Added

• Added CHANGELOG.md

Fixed

• Fixed bug in coverage where writing to non-bedgraph files would result in an error

[0.4.4] - 2024-04-5

Changed

• finaletools.frag.coverage accepts Frag.gz format files
• update CLI help messages and docstrings for coverage and DELFI to reflect current and previous changes
• update docs

[0.4.2] - 2024-03-28

Changed

• Updated emails in pyproject.toml