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Project description
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
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