Skip to content

sem0036/MARTIN_Project2

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

3 Commits
 
 
 
 
 
 

Repository files navigation

Project 2

Sarah Martin

Run in bash

#!/bin/bash

Input file

ADH.fa

Output file

GCcount.txt

This code performs as a GC calculator when run with a fasta file

Total number of sequences

seq=$(grep -c ">" $1)

Arrays for name of sequence and actual sequence

sequencename=($(grep ">" $1 | cat))
sequence=($(grep -v '>' $1 | cat))

For loop to calculate GC percentage and insert it into GCcount.txt

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

Table of percentages for input file

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

About

No description, website, or topics provided.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages