pango-collapse 0.4.0

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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 compressed lineage will be returned. Collapsed up to either A or B by add A and B to the collapse file. By default (i.e. if no collapse file is specified) pango-collapse uses the collapse file found here. This file is dependant on the version of pango-collapse, use --latest to use the latest version on the collapse file at run time.

# 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,BA.4.6
BE.1,B.1.1.529.5.3.1.1,BE.1

Nextclade example

This example shows how to use some of the pango-collapse features by collapsing the Pango Lineages in the output from Nextclade.

Produce a nextclade.tsv file from a nextclade analysis (there is an example file in tests/data.

We are only interested in the major sub-lineages of omicron i.e. BA.1-BA.5. We can therefor make a collapse file with the following:

# omicron
BA.1
BA.2
BA.3
BA.4
BA.5

Note: BA is an alias of B.1.1.529, however, as we have not included B.1.1.529 in our collapse file any samples designated B.1.1.529 will not be compressed.

Run the following command to collapse the omicron sub-lineages:

pango-collapse nextclade.tsv -o nextclade_collapsed_omicron.tsv -l Nextclade_pango --strict 

The -l (--lineage-column) flag tells pango-collapse to look for the compressed linage in the Nextclade_pango column in the nextclade.tsv file.

The --strict tells pango-collapse to use strict mode i.e. only report lineages in the collapse file. If the lineage cannot be collapsed then no value is returned in the collapse column.

We can visualise the results in pandas:

import pandas as pd
df = pd.read_csv("nextclade_output.tsv", sep="\t")
df.Lineage_family.fillna('Other', inplace=True)
df.Lineage_family.value_counts().plot(kind='bar')