pango-collapse 0.3.4

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Pango-collapse

CLI to collapse Pango linages for reporting

Install

Install from pypi with pip.

pip install pango-collapse

Usage

pango-collapse takes a CSV file of SARS-CoV-2 samples (input.csv) with a column (default Lineage) indicating the pango lineage of the samples (e.g. output from pangoLEARN, nextclade, USHER, etc).

# input.csv
Lineage
BA.5.2.1
BA.4.6
BE.1

pango-collapse will collapse lineages up to the first user defined parent lineage (specified in a text file with --collapse-file). If the sample lineage has no parent lineage in the user defined collapse file the lineage will be collapsed up to either A or B. By default pango-collapse uses the collapse file found here.

# collapse.txt
BA.5
BE.1

pango-collapse will produce an output file which is a copy of the input file plus Lineage_full (the uncompressed lineage) and Lineage_family (the lineage compressed up to) columns.

pango-collapse input.csv --collapse-file collapse.txt -o output.csv 

# output.csv 
Lineage,Lineage_full,Lineage_family
BA.5.2.1,B.1.1.529.5.2.1,BA.5
BA.4.6,B.1.1.529.4.6,B
BE.1,B.1.1.529.5.3.1.1,BE.1