improvement: use wc to count bp instead of summing contig header info for abundance

[franciscozorrilla]

For abundance calculation we need to get bp of genome, currently we do this based on the contig headers info, although this can become problematic for genomes assembled by different tools (e.g. shovill renames them iirc). Replace this with a simple wc command to count bases in fasta

metaGEM/workflow/Snakefile

Lines 1118 to 1124 in a4daea0

	# Check if bins are original (megahit-assembled) or strict/permissive (metaspades-assembled)
	if [[ $bin == *.strict.fa ]] || [[ $bin == *.permissive.fa ]] || [[ $bin == *.s.fa ]] || [[ $bin == *.p.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

[franciscozorrilla]

Temporary workaround to deal with megahit, shovil, and metaGEM outputs

# Check if bins are original (megahit-assembled) or strict/permissive (metaspades-assembled)
            if [[ $bin == *.strict.fa ]] || [[ $bin == *.permissive.fa ]] || [[ $bin == *.s.fa ]] || [[ $bin == *.p.fa ]];then
                less $bin |grep ">"|cut -d '_' -f4|awk '{{sum+=$1}}END{{print sum}}' >> $(echo "$bin"|sed "s/.fa/.map/")
            elif [[ $bin == *.shovill.fa ]];then
                less $bin |grep ">"|cut -d ' ' -f2|sed 's/len=//g'|awk '{{sum+=$1}}END{{print sum}}' >> $(echo "$bin"|sed "s/.fa/.map/")
            elif [[ $bin == *megahit.fa ]];then
                less $bin |grep ">"|cut -d '-' -f4|sed 's/len=//g'|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

Rather than keep extending this for each possible case, just use wc to count bp after removing newlines

genome.fa|grep -v '>'|tr -d '\n'|wc -m