Introduction to Reading Files Line by Line in Bash

Bash provides several ways to read files line by line, which is a common task in shell scripting. In this tutorial, we will explore the different methods of reading files line by line in Bash.

Method 1: Using a While Loop with Read

The most common method of reading a file line by line in Bash is by using a while loop with the read command. Here’s an example:

filename='peptides.txt'
echo "Start"
while read -r p; do
    echo "$p"
done < "$filename"

In this example, the while loop reads each line from the file peptides.txt and stores it in the variable p. The -r option tells read to disable backslash escaping.

Method 2: Using a For Loop with Cat

Another method of reading a file line by line is by using a for loop with the cat command. Here’s an example:

filename='peptides.txt'
echo "Start"
for word in $(cat "$filename"); do
    echo "$word"
done

However, this method has some limitations. It splits the input on whitespace characters, which can cause issues if your file contains spaces or tabs.

Method 3: Using a While Loop with Read and IFS

To avoid splitting on whitespace characters, you can use the IFS (Internal Field Separator) variable to specify the delimiter. Here’s an example:

filename='peptides.txt'
echo "Start"
while IFS= read -r p; do
    echo "$p"
done < "$filename"

In this example, IFS= sets the internal field separator to nothing, so the entire line is read into the variable p.

Reading from a Delimited File

If your file is delimited by a specific character (e.g., comma or colon), you can use the read command with the -d option to specify the delimiter. Here’s an example:

filename='input.txt'
echo "Start"
while IFS=: read -r field1 field2 field3; do
    echo "$field1 $field2 $field3"
done < "$filename"

In this example, IFS=: sets the internal field separator to a colon, so each line is split into three fields.

Reading from the Output of Another Command

You can also read from the output of another command using process substitution. Here’s an example:

echo "Start"
while read -r line; do
    echo "$line"
done < <(command ...)

In this example, <(command ...) is a process substitution that runs the command and pipes its output to the while loop.

Reading a Whole File into an Array

If you need to read a whole file into an array, you can use the readarray command (available in Bash 4.x and later). Here’s an example:

filename='my_file.txt'
echo "Start"
readarray -t my_array < "$filename"
for line in "${my_array[@]}"; do
    echo "$line"
done

In this example, readarray reads the entire file into the array my_array, and then you can iterate over the array using a for loop.

Conclusion

Reading files line by line is a common task in shell scripting. Bash provides several methods to achieve this, including using a while loop with read, a for loop with cat, and reading from a delimited file or the output of another command. By choosing the right method for your specific use case, you can efficiently read files line by line in Bash.