generate_epiToPublicAndDate.py

#!/usr/bin/env python
# coding: utf-8

# Preprocess files for parsing

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import pandas as pd


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gisaid_meta = pd.read_csv("results/gisaid/metadata_2022_08_08.tsv.gz", sep="\t")


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gisaid_meta["vname"] = gisaid_meta["Virus name"].str.replace("hCoV-19/","")
gisaid_meta["vname2"] = gisaid_meta["vname"]


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epi_map = gisaid_meta[["Accession ID", "vname", "vname2", "Collection date"]]


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epi_map = epi_map.sort_values(by="Accession ID", ascending = True)


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epi_map


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epi_map.to_csv("results/gisaid/epiToPublicAndDate.latest", header=False, sep="\t", index=False)


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# get_ipython().run_line_magic('pinfo', 'pd.to_csv')


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get_ipython().run_line_magic('pinfo', 'pd.DataFrame.to_csv')


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