INNER CODE UNIT · Python

binAbundanceFraction

franciscozorrilla/metaGEM · workflow/rules/Snakefile_single_end.smk.py:807

        binAbundanceFraction = ( X / Y / Z) * 1000000

        X = # of reads mapped to bin_i from sample_k
        Y = length of bin_i (bp)
        Z = # of reads mapped to all bins in sample_k

        Note: 1000000 scaling factor converts length in bp to Mbp

        """
    shell:
        """
        set +u;source activate {config[envs][metabagpipes]};set -u;
        mkdir -p {output}
        cd $TMPDIR

        echo -e "\nCopying quality filtered single end reads and generated MAGs to TMPDIR ... "
        cp {input.READS} {input.bins}/* .

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