INNER CODE UNIT · Python

$name

franciscozorrilla/metaGEM · workflow/rules/Snakefile_single_end.smk.py:644

                if [[ $name == *.strict ]] || [[ $name == *.permissive ]];then
                    L=$(less $bin |grep ">"|cut -d '_' -f4|awk '{{sum+=$1}}END{{print sum}}')
                else
                    L=$(less $bin |grep ">"|cut -d '-' -f4|sed 's/len_//g'|awk '{{sum+=$1}}END{{print sum}}')
                fi

                echo "Reading bin $bin ... Contigs: $N , Length: $L "
                echo $name $N $L >> reassembled_bins.stats;
            done;
        done
        echo "Done reading metawrap reassembled bins ... "

        # READ METAWRAP REFINED CHECKM OUTPUT  

        echo "Generating CheckM summary file reassembled.checkm across samples for reassembled bins ... "
        for folder in */;do 
            var=$(echo $folder|sed 's|/||g');
            paste $folder*reassembled_bins.stats|tail -n +2|sed "s/^/$var./g";

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