0.0.21 #34
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0.0.21 #34
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modification to trim non-identical edges from the linking step. So now, it should be less like a ball of yarn unless there really is only identical sequences
Updated the preprocessing format to be consistent with AssignGenes.py and MakeDb.py behaviour from changeo
bug fix
minor QoL change
bug fix
bug fix
wow found a bug that i didn't think of
Fixed bug where format_fasta wasn't properly trimming the trailing hypen number. Overhauled the reannotation functions to now produce both blast and airr format outputs. Commented out the code that was handling insertion of gaps in airr output. The amino acid sequence alignments from airr output will be lifted onto the blast output file as a final step.
bug fix
testing if commenting out the neighbors key works
changed default metric for gini to use closeness centrality rather than degree
bug fix
added option to plot bar plots by restricting to clone size
bug fix
bug fix
bug fix
bug fix for saving incredibly big files
adjust creation of tmp files
change error reporting
merge more columns from airr output
bug fix
bug fix
bug fix
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Fixed bug where contigs that were assigned with light chain V/D/J but with a heavy chain constant and vice versa were not picked up during filter_bcr
Fixed bug where rpy2 couldn't read/convert data frame
Fixed and updated database versions.
Rehauled preprocessing steps for reannoate_genes; now both airr and changeo formats are created in tmp folder and the two dataframes are merged prior to reassign_isotype.
Removed the automatic population of .uns slot in anndata during transfer.
New pl.clone_overlap function to visualise clone overlap between samples as a circos plot.