INNER CODE UNIT · Python

nSpecies

franciscozorrilla/metaGEM · workflow/rules/Snakefile_experimental.smk.py:393

        nSpecies=$(ls $(basename {output})|wc -l)
        nSpeciesTot=$(cat $(basename {output})/*|wc -l)
        nMAGsTot=$(paste {input.binning}|wc -l)
        echo -e "\nIdentified $nSpecies species represented by at least 10 high quality MAGs, totaling $nSpeciesTot MAGs out of $nMAGsTot total MAGs generated ... "

        echo -e "\nMoving speciesBinIDs folder to pangenome directory: $(dirname {output})"
        mv $(basename {output}) $(dirname {output})

        echo -e "\nOrganizing prokka folder according to taxonomy ... "
        echo -e "\nGFF files of identified species with at least 10 HQ MAGs will be copied to prokka/organzied/speciesSubfolder for roary input ... "
        cd $(dirname {output})
        mkdir -p prokka/organized

        for species in speciesBinIDs/*.txt;do

            speciesID=$(echo $(basename $species)|sed 's/.txt//g');
            echo -e "\nCreating folder and organizing prokka output for species $speciesID ... "
            mkdir -p prokka/organized/$speciesID

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