Guys, I've got a .fasta file , with the usual scheme

>NODE XX _ lenght XX_cov.xx.xx
ACGACGACGACACTCTACAGATACGACAT
>NODE YY_lenght YY_cov.YY.YY
CGACGACATCAGCATACAGATACTA

I wrote a small script to get the GC content of each contig sequence, and so on, to convert the "cov." value expressed into the nucleotidic coverage. Here's the code

    #! /bin/bash

## 
## This script needs to do few things: 
##
## First of all, conversion of cov with nucleotidic one

# Parameters options

display_help() {
    echo "Usage: $0 [file.fasta] [option..]" >&2
    echo
    echo "  -k, --kmer  kmer last value"
    echo "  -l, --lenght    read lenght"
    echo 
    echo "  example: $0 file.fasta -k 77 -l 150"
    echo 
    exit 1
}



case "$1" in 
    -h | --help )
        display_help
        exit 0
        ;;
esac 

case "$2" in
    -k | --kmer )
        KMER=($3)
        ;;
esac 

case "$4" in            
    -l | --lenght)
        READLENGHT=($5)
        ;;
esac 



# Check if the format is correct
if [[ $1 != *.fasta ]]; then
    echo "The input file $1 it's not in fasta format!"
    echo ""    
    echo "Usage: ./nomescript.sh NO_HIT.fasta"
  exit 1
fi



# calculate the coefficient used to convert coverage. Final is Y 
# calculate GC content of each sequence 

K=$(($READLENGHT - $KMER + 1))
Y=$(echo "scale=4; $K / $READLENGHT" | bc)

while read odd; do
    echo -n "${odd##}" | cut -d "_" -f 1,2,3,4 && printf "nucleotide_cov: " 
    echo "scale=4;${odd##*_} / $Y" | bc 
    read even
    echo "${even##}" &&
    ACOUNT=$(echo "${even##}" |  sed -e "s/./&\n /g" | grep -c "A")  
    GCOUNT=$(echo "${even##}" |  sed -e "s/./&\n /g" | grep -c "G")
    CCOUNT=$(echo "${even##}" |  sed -e "s/./&\n /g" | grep -c "C")
    TCOUNT=$(echo "${even##}" |  sed -e "s/./&\n /g" | grep -c "T")
    TOTALBASES=$(($ACOUNT+$GCOUNT+$CCOUNT+$TCOUNT))
    GCCONT=$(($GCOUNT+$CCOUNT))
    printf "GC_CONT: " 
    echo "scale=2;$GCCONT / $TOTALBASES *100" | bc  
done < "$1"

It actually does the work, stamping a file like:

>NODE 
nucleotide_cov:
ACGACGAATCATACGACATAA
GC_CONT: 
>NODE
nucleotide_cov
GCAGCATACATCAGATACGATAC
GC_CONT

My problem is that is extremely slow when it works against .fasta > 200Mb.

I'm looking for a way to increase its speed, or doing the same work with other kind of script. Maybe.. python?