#!/bin/bash
ADH.fa
GCcount.txt
seq=$(grep -c ">" $1)
sequencename=($(grep ">" $1 | cat))
sequence=($(grep -v '>' $1 | cat))
for ((i=0; i<$seq; i++))
do
G="$(echo ${sequence[$i]} | grep -o 'G' | wc -l)"
C="$(echo ${sequence[$i]} | grep -o 'C' | wc -l)"
GC=$(echo $G+$C | bc -l)
total=$(echo ${sequence[$i]} | wc -m)
percent=$(echo "scale=2 ; ($GC/$total)" | bc)
echo "${sequencename[$i]} $percent" >> GCcount.txt
done
Sequence Name | GC Percentage |
---|---|
>DI245396.1 | 43 |
>DI245395.1 | 42 |
>HW262829.1 | 43 |
>546218138 | 42 |
>X13802.1 | 39 |
>NM_001179558.3 | 51 |
>NM_001178613.2 | 45 |
>AY558240.1 | 51 |
>AB052924.1 | 51 |