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Update 03-horizontalGeneTransfer-TDA.md
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nselem authored Apr 13, 2024
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{: .challenge}
>
Firs we will read the _S. agalactiae_ resistance genes that
First, we will read the _S. agalactiae_ resistance genes that
we obtained in the episode [Annotating Genomic Data](https://carpentries-incubator.github.io/pangenomics/03-annotation-with-Prokka/index.html), from the lesson [Pangenome Analysis in Prokaryotes](https://carpentries-incubator.github.io/pangenomics/index.html).
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link="https://raw.githubusercontent.com/carpentries-incubator/topological-data-analysis/gh-pages/files/agalactiae_card_full.tsv"
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{: .output}

Now, we will obtained the values from the dataframe.
Now, we will obtain the values from the data frame.
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values=df_transposed_new.iloc[:,:].values
~~~
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{: .output}

> ## Exercise 2: Persistent homology of _S. agalactiae_ resistome
> Fill in the blanks with the following parameters to calculate the persisten homology of the _S. agalactiae_ resistome.
> Fill in the blanks with the following parameters to calculate the persistent homology of the _S. agalactiae_ resistome.
> hamming_matrix_3, values, calculate_hamming_matrix, create_complex
>
> ~~~
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