pytximport 0.11.0

API

• Added a CLI interface for transcript-to-gene mappings
• Expanded filter_by_biotype to work with already gene-level summarized objects as well
• Added multi-target support to create_transcript_to_gene_map and create_transcript_gene_map_from_annotation

Other changes

• Fixed bug when importing oarfish data
• Added link to manuscript

pytximport 0.10.0

API

• Added experimental support for SummarizedExperiment as output_type/output_format
• Fixed an RSEM bug where a minimum length requirement of 1 was not being enforced

pytximport 0.9.0

API

• Added support for .csv transcript to gene maps
• Added experimental inferential replicate support for oarfish and psicem quantification files
• Moved ignore_bar and ignore_transcript_version logic from utils.convert_transcripts_to_genes to core.tximport

Other changes

• General performance improvements
• Vectorized get_median_length_over_isoform
• Added support for pyarrow for reading in .tsv/.csv files
• Removed unnecessary copy operations
• Added support for .csv transcript to gene maps
• Added test for RSEM and Piscem files
• Updated the documentation to include recommendations for installation options and added code examples to docstrings

pytximport 0.8.0

API

• Allows the source column and the target column from the GTF to be explicitly set when creating a transcript-to-gene or transcript-name-to-transcript-mapping
• Removes unused sparse and sparse_threshold arguments

Other changes

• Adds regular cron job CI testing to detect changed dependencies

pytximport 0.7.0

API

• Added support for RSEM gene-level quantification files. Previously, it was already possible to read RSEM transcript level data from a .tsv file. Now, not only can RMEM transcript data be read in by setting data_type to rsem, but if gene_level is set to True, existing gene-level data can be read in and aggregated by pytximport.
• Added support for gzipped files when reading in tabular data with data_type set tsv.

Other changes

• pytximport is now available through Bioconda and an install badge has been added to the README and the documentation.
• Added unit tests to check RSEM gene-level quantification for correctness.

pytximport 0.6.0

API

• Added utility functions to create transcript-to-gene maps from Biomart or .gtf files.
• Added a flag to allow overwriting existing files.

Other changes

• Added unit tests for file saving via programatic (non-CLI) usage.

pytximport 0.5.0

API

• Added support for inferential replicates via the inferential_replicates, inferential_replicate_variance and inferential_replicate_transformer arguments with support for salmon and kallisto.
• Fixed a bug where custom column names were not applied.
• Fixed a bug when saving .csv files from AnnData objects.

Other changes

• Added unit tests for file saving via programatic (non-CLI) usage.

pytximport 0.4.0

API

• Added a new count transformation for differential transcript usage analysis: dtu_scaled_tpm (dtuScaledTPM in R-version of tximport)
• Added a utility function for renaming transcript-level exports with the transcript name: utils.replace_transcript_ids_with_names.
• When using biotype filtering, the TPM values will now be rescaled to match the sum of the TPM values before filtering.
• Apply biotype filtering, ignore transcript version and ignore after bar for transcript-level exports as well.
• Bug fix: Saving to files when exporting transcript-level counts works now.

Other changes

• Moved transcript version removal into the utility function remove_transcript_version and biotype filtering into the utility function filter_by_biotype.
• Always run unittests locally for each commit with pre-commit.

pytximport 0.3.0

API

• Change the default output_type to "anndata".
• When a biotype filter is used, the abundance of the remaining transcripts after filtering will now be rescaled to match the total abundance pre-filtering for each sample.
• Bug fix: Now returns AnnData objects when returning transcript-level data if output_type is "anndata".

Other changes

• Run CI on dev branch.

pytximport 0.2.0

API

• Automatically change output_type to anndata if output_format is h5ad and warn the user if a different output_type was provided.

Other changes

• Add a unit test that tests for correctness against the R version of tximport (version 1.32.0).
• Release versions via GitHub actions.