Releases: complextissue/pytximport
Releases · complextissue/pytximport
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
torsem
, but ifgene_level
is set to True, existing gene-level data can be read in and aggregated bypytximport
. - Added support for gzipped files when reading in tabular data with
data_type
settsv
.
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
andinferential_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 oftximport
) - 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 functionfilter_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
toanndata
ifoutput_format
ish5ad
and warn the user if a differentoutput_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.