compare_annotations

compare_annotations compares annotations produced by digger with IMGT’s annotations as summarised by parse_annotations. Three files are produced: - a .jpg showing Venn diagrams of identified functional annotations - a .txt file summarising the specific functional sequences that were only identified in one annotation as opposed to both - a .csv file listing agreements and differences of all sequences annotated by either mmethod Please refer to Annotating the human IGH locus for example usage.

Compare digger results to an IMGT annotation

usage: compare_annotations [-h] [-nc] [--filter_annot FILTER_ANNOT] [--comp_name COMP_NAME] [--target_locus TARGET_LOCUS]
                           digger_results annotation_file sense outfile

Positional Arguments

digger_results

Digger results file

annotation_file

IMGT annotation produced by parse_imgt_assembly_x.py

sense

Sense of annotation compared to digger results (forward or reverse)

outfile

Output file name (will create .csv, .jpg, .txt

Named Arguments

-nc

include sequences for leader and rss

Default: False

--filter_annot

filter IMGT annotations by sense (forward or reverse)

--comp_name

name to use for comparison (default IMGT)

--target_locus

Only consider IMGT matches to the target locus (used for TRA/TRD)