INNER CODE UNIT · Python

$bin

franciscozorrilla/metaGEM · workflow/rules/Snakefile_single_end.smk.py:875

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

            paste $(echo "$bin"|sed "s/.fa/.map/")

            echo -e "\nCalculating abundance for bin $bin ... "
            echo -n "$bin"|sed "s/.fa//" >> $(echo "$bin"|sed "s/.fa/.abund/")
            echo -n $'\t' >> $(echo "$bin"|sed "s/.fa/.abund/")

            X=$(less $(echo "$bin"|sed "s/.fa/.map/")|grep "mapped ("|awk -F' ' '{{print $1}}')
            Y=$(less $(echo "$bin"|sed "s/.fa/.map/")|tail -n 1|awk -F' ' '{{print $4}}')
            Z=$(less "../map.stats"|grep "mapped ("|awk -F' ' '{{print $1}}')
            awk -v x="$X" -v y="$Y" -v z="$Z" 'BEGIN{{print (x/y/z) * 1000000}}' >> $(echo "$bin"|sed "s/.fa/.abund/")
            
            paste $(echo "$bin"|sed "s/.fa/.abund/")

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