How to find gc content of a fasta file using bash script? - linux

Question

I am learning bioinformatics.
I want to find GC content from a fasta file using Bash script.
GC content is basically (number of (g + c)) / (number of (a + t + g + c)).
I am trying to use wc command. But I was not able to get an answer.
Edit 17th Feb 2023.
After going through documentation and videos, I came up with a solution.
filename=$# # collecting all the filenames as parameters
for f in $filename # Looping over files
do
echo " $f is being processed..."
gc=( $( grep -v ">" < "$f" | grep -io 'g\|c'< "$f" | wc -l)) # Reading lines that dont start with < using -v. grep -io matches to either g or c and outputs each match on single line. wc -l counts the number of lines or indirectly the number of g and c. This is stored in a variable.
total=( $( grep -v ">" < "$f" | tr -d '\s\r' | wc -c)) # Spaces, tabs, new line are removed from the file using tr. Then the number of characters are counted by wc -c
percent=( $( echo "scale=2;100*$gc/$total" |bc -l)) # bc -l is used to get the answer in float format. scale=2 mentions the number of decimal points.
echo " The GC content of $f is: "$percent"%"
echo
done

Answer 1

Do not reinvent the wheel. For common bioinformatics tasks, use open-source tools that are specifically designed for these tasks, are well-tested, widely used, and handle edge cases. For example, use EMBOSS infoseq utility. EMBOSS can be easily installed, for example using conda.
Example:
Install EMBOSS package (do once):
conda create --name emboss emboss --channel iuc
Activate the conda environment and use EMBOSS infoseq, here to priitn the sequence name, length and percent GC:
source activate emboss
cat your_sequence_file_name.fasta | infoseq -auto -only -name -length -pgc stdin
source deactivate
This prints into STDOUT something like this:
Name Length %GC
seq_foo 119 60.50
seq_bar 104 39.42
seq_baz 191 46.60
...

Answer 2

This should work:
#!/usr/bin/env sh
# Adapted from https://www.biostars.org/p/17680
# Fail on error
set -o errexit
# Disable undefined variable reference
set -o nounset
# ================
# CONFIGURATION
# ================
# Fasta file path
FASTA_FILE="file.fasta"
# Number of digits after decimal point
N_DIGITS=3
# ================
# LOGGER
# ================
# Fatal log message
fatal() {
printf '[FATAL] %s\n' "$#" >&2
exit 1
}
# Info log message
info() {
printf '[INFO ] %s\n' "$#"
}
# ================
# MAIN
# ================
{
# Check command 'bc' exist
command -v bc > /dev/null 2>&1 || fatal "Command 'bc' not found"
# Check file exist
[ -f "$FASTA_FILE" ] || fatal "File '$FASTA_FILE' not found"
# Count number of sequences
_n_sequences=$(grep --count '^>' "$FASTA_FILE")
info "Analyzing $_n_sequences sequences"
[ "$_n_sequences" -ne 0 ] || fatal "No sequences found"
# Remove sequence wrapping
_fasta_file_content=$(
sed 's/\(^>.*$\)/#\1#/' "$FASTA_FILE" \
| tr --delete "\r\n" \
| sed 's/$/#/' \
| tr "#" "\n" \
| sed '/^$/d'
)
# Vars
_sequence=
_a_count_total=0
_c_count_total=0
_g_count_total=0
_t_count_total=0
# Read line by line
while IFS= read -r _line; do
# Check if header
if printf '%s\n' "$_line" | grep --quiet '^>'; then
# Save sequence and continue
_sequence=${_line#?}
continue
fi
# Count
_a_count=$(printf '%s\n' "$_line" | tr --delete --complement 'A' | wc --bytes)
_c_count=$(printf '%s\n' "$_line" | tr --delete --complement 'C' | wc --bytes)
_g_count=$(printf '%s\n' "$_line" | tr --delete --complement 'G' | wc --bytes)
_t_count=$(printf '%s\n' "$_line" | tr --delete --complement 'T' | wc --bytes)
# Add current count to total
_a_count_total=$((_a_count_total + _a_count))
_c_count_total=$((_c_count_total + _c_count))
_g_count_total=$((_g_count_total + _g_count))
_t_count_total=$((_t_count_total + _t_count))
# Calculate GC content
_gc=$(
printf 'scale = %d; a = %d; c = %d; g = %d; t = %d; (g + c) / (a + c + g + t)\n' \
"$N_DIGITS" "$_a_count" "$_c_count" "$_g_count" "$_t_count" \
| bc
)
# Add 0 before decimal point
_gc="$(printf "%.${N_DIGITS}f\n" "$_gc")"
info "Sequence '$_sequence' GC content: $_gc"
done << EOF
$_fasta_file_content
EOF
# Total data
info "Adenine total count: $_a_count_total"
info "Cytosine total count: $_c_count_total"
info "Guanine total count: $_g_count_total"
info "Thymine total count: $_t_count_total"
# Calculate total GC content
_gc=$(
printf 'scale = %d; a = %d; c = %d; g = %d; t = %d; (g + c) / (a + c + g + t)\n' \
"$N_DIGITS" "$_a_count_total" "$_c_count_total" "$_g_count_total" "$_t_count_total" \
| bc
)
# Add 0 before decimal point
_gc="$(printf "%.${N_DIGITS}f\n" "$_gc")"
info "GC content: $_gc"
}
The "Count number of sequences" and "Remove sequence wrapping" codes are adapted from https://www.biostars.org/p/17680
The script uses only basic commands except for bc to do the precision calculation (See bc installation).
You can configure the script by modifying the variables in the CONFIGURATION section.
Because you haven't indicated which one you want, the GC content is calculated for both each sequence and the overall. Therefore, get rid of anything that isn't necessary :)
Despite my lack of bioinformatics background, the script successfully parses and analyzes a fasta file.