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@zktuong zktuong released this 17 Jun 12:07
· 998 commits to master since this release
v0.1.3
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Learn about vigilant mode.

Updates

  • Adjusted names and functions to allow for TCR data in AIRR format to be handled. Instead of heavy/light, the naming convention will be using VDJ/VJ - consistent with how scirpy names the columns. Same goes for mentions of BCR is renamed to contig where appropriate.
  • Renamed function name from filter_bcr to filter_contigs.
  • Added option for filename_prefix to control the behaviour during the preprocessing step better.
  • Updates should work with recently merged PR to modify the container script.
  • filter_contigs have been partially reworked - no longer require a multiple core implementation as the new implemenation now runs faster without it.
  • umi_count is now treated as a back up to duplicate_count if there is modification of the duplicate_count due to filter_contigs.
  • Added locus option to filter_contigs so that it can work with the new implementation of the data class.
  • Singularity container now has additional options to trigger tr pre-processing mode. Kudos to Krzysztof #80.
  • Rewrote tests to stop downloading files everytime it needs to start a test.
    • This lets me write very specific tests! Will have to expand on this eventually.

Bug Fix

  • Remove extra filtering section in single-core implementation of filter_contig.
  • make the umi_count vs duplicate_count behaviour more consistent. Now duplicate_count is the default column.

Ongoing

  • Tests are failing for the preprocess script. Perhaps I should break it up to find out exactly what's wrong. Readthedocs is also complaining that Command killed due to excessive memory consumption.
  • Rewriting unit tests. Seems like they are working so far (minus some typos here and there)
  • Need to add in more detailed tests.
  • Need to add in tests to switch data with scirpy. Also need to write native 10x data parser to reduce reliance on scirpy.

Known issues

  • The current instructions to use singularity comes with a few issues if ~/.bash_rc is present:
    • If the ~/.bash_rc is present and within it comes with conda initialization code, then the default conda path will be appended to the front of the container's $PATH. This impacts on users who install igblast and blast via conda + also want to use the container. What will happen is that the container will try to use the blast outside the container first, which may then lead to issues where it cannot find the database files.
    • Specifying --no-home doesn't solve the issue completely as scanpy requires a writeable numba_cache_dir. Currently the container will hopefully try to create a $PWD/dandelion_cache folder if this is an issue but needs more testing.

Still needs work

#54 Check productive_only option in filter_bcr
#62 Streamline update_metadata
#63 Fix update_metadata to work with concat.
#64 Allow retrieve to work both ways
#68 Native implementation of function to count mutation
#69 Rescue contigs that fail germline reconstruction?
#70 Check for compatibilty with mouse data

Assets 2