Awk interleaved files

Please write comments if you find anything incorrect, or you want to share more information about the topic discussed above. Skip to content. Change Language. Related Articles. Table of Contents. Improve Article. Save Article. Like Article. Next cut command in Linux with examples. It only takes a minute to sign up. Connect and share knowledge within a single location that is structured and easy to search. How do I take two input files and create an output file that interleaves their contents?

For example, if one file contains:. Sign up to join this community. The best answers are voted up and rise to the top. Stack Overflow for Teams — Collaborate and share knowledge with a private group.

Create a free Team What is Teams? Note: The awk command got its name from three people who wrote the original version in - Alfred A ho, Peter W einberger, and Brian K ernighan.

Some of the available operations are:. The if-else statement works by evaluating the condition specified in the parentheses and, if the condition is true, the statement following the if statement is executed. The else part is optional. The output shows the lines in which duplicates exist and states No duplicates if there are no duplicate answers in the line.

The while statement repeatedly executes a target statement as long as the specified condition is true. That means that it operates like the one in the C programming language. If the condition is true, the body of the loop is executed. If the condition is false, awk continues with the execution. For example, the following statement instructs awk to print all input fields one per line:.

The for statement also works like that of C, allowing users to create a loop that needs to execute a specific number of times. The statement above increases the value of i by one until it reaches ten and calculates the square of i each time.

The operators are grouped with parentheses. The break statement immediately exits from an enclosing while or for. To begin the next iteration, use the continue statement. The next statement instructs awk to skip to the next record and begin scanning for patterns from the top. The exit statement instructs awk that the input has ended. Note: The awk tool allows users to place comments in AWK programs. Comments begin with and end at the end of the line.

On the commandline however it is a lot easier to work with a fasta file where the sequence spans just a single line. The following command snippet allows you to convert you the interleaved format to the single line format using awk, which is installed on most Linux systems by default. Receive updates about NGS articles and trainings. We can help you to get the most out of your sequencing experiments by developing data analysis strategies and expert consulting.