Reading a Single File from a tar Archive You can extract and display a single file’s content from a tar archive without unpacking the entire archive using tar‘s standard output option. Basic Syntax tar -xOf archive.tar.gz path/to/file The key flags are: -x: Extract files from the archive -O (capital O): Write extracted files to standard…
Printing Fields After a Specified Column with awk When processing text data, you often need to extract everything from a certain field onward. awk makes this straightforward once you understand the mechanics. Basic Syntax The fundamental approach uses awk’s field variables and looping: awk ‘{for(i=N;i<=NF;i++) printf “%s “, $i; print “”}’ file.txt Replace N with…
Counting Reads Per Chromosome in BAM Files BAM files store aligned sequence reads in a compressed binary format. Counting reads by chromosome is a common task in genomics workflows—useful for quality control, coverage analysis, and identifying potential sequencing biases. Using samtools idxstats The fastest and most straightforward approach is samtools idxstats, which requires an indexed…
Extracting and Removing Trailing Numbers from Strings Extracting or removing trailing numbers from strings is a common task in shell scripting. Whether you’re parsing log files, processing configuration values, or cleaning up filenames, you’ll need reliable methods to handle these operations. Using Parameter Expansion The cleanest approach uses bash parameter expansion, which doesn’t require external…
Joining multiple lines from a file in Bash The most common need is collapsing multi-line records into single lines. Here are the practical approaches: Using tr to remove newlines The simplest method removes all newlines: tr -d ‘\n’ < input.txt > output.txt This works well for data without embedded line breaks you want to preserve….
Matching tabs with grep Grep handles tab characters in a few different ways depending on your needs. Here’s what actually works. Using \t with extended regex The most straightforward approach uses grep’s extended regular expressions (-E flag): grep -E ‘\t’ filename.txt This matches any line containing a literal tab character. The \t escape sequence is…
Getting CPU Temperature on Linux Most modern systems have thermal sensors built into the CPU and motherboard. Reading these sensors is essential for monitoring system health, diagnosing performance issues, and preventing thermal throttling or hardware damage. Install lm-sensors The standard tool for reading hardware sensors on Linux is lm-sensors. Install it on your system: Debian/Ubuntu:…
I have a text file with many lines of text. In Linux, how to sort the lines by their length? You can make use of awk together with the sort program like awk ‘{ print length(), $0 | “sort -n” }’ /path/to/text/file Here, we use awk to calculate the text length and sort -n to…
How to cut by multiple spaces in Linux? For example, if I get a string like a b c d where the spaces among the fields are not decided. How to get the four fields a, b, c and d out? Here, we take getting ‘b’ (the 2nd field) as the example. You can first…
How to exclude last N columns of a string in bash? The point is that the number of columns in each line is uncertain (but > N). For example, I would like to remove the last 2 columns separated by ‘.’ in the following lines. systemd.3.gz systemd.mount.3.gz systemd.mount.f.3.gz The simple cut command cut -d’.’ -f1…
How to calculate the average of value in lines of a text file on Linux by a script? The file.txt is like: Run 0: Time used: 22.235331711 seconds. Run 1: Time used: 20.784491219 seconds. Run 2: Time used: 21.851638876 seconds. What I want it to calculate the average time. awk is handy for this purpose:…
The Problem: cut Only Accepts Single-Character Delimiters The cut command is designed for simple field splitting, but it has a hard limitation: the delimiter must be a single character. cut –delimiter=”delim” -f 1,3 # Error: cut: the delimiter must be a single character This is a deliberate design choice. cut prioritizes speed and simplicity for…
Padding Integers with Leading Zeros in Bash When you need to format an integer with leading zeros in bash, printf is the standard approach. This is useful for generating zero-padded IDs, filenames, or any formatted output. Using printf The basic syntax mirrors C’s sprintf: n=42 str=$(printf “%08d” “$n”) echo “$str” # Output: 00000042 Here, %08d…
Removing Untracked Files from SVN Working in an SVN repository often leaves behind temporary build artifacts, compiled outputs, and editor cache files. Unlike Git’s git clean command, SVN has no built-in cleanup mechanism for untracked files. Using svn st to Identify Untracked Files The svn status command (or svn st) marks untracked files with a…
Checking if Servers Are Alive with a Bash Script When managing multiple servers, you’ll inevitably deal with hosts that go down, get rebooted, or become unreachable. While orchestration tools like Kubernetes and Ansible handle this at scale, a simple Bash script using ping works well for quick checks or smaller deployments. Basic Approach The core…