How to print all fields after a certain field with awk on Linux? Say, I want to print out all fields after field $3: a b c d e f a b b b a a c d should be transformed to d e f b d You may use a for loop in awk…
How to count the number of reads in each chromosome in a bam file? The bam file is already sorted by the chromosome names. If the bam file is indexed, you may quickly get these info from the index: samtools idxstats in.bam | awk ‘{print $1″ “$3}’ If the bam file is not indexed, you…
Most modern servers or computers have sensors to detect the temperature of various components. On Linux, how to get the CPU core temperatur in command linux? First, make sure the package “lm-sensors” is installed on your Linux and the command sensors works for you. Then, you can use this piece of script to get the…
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:…
Is is possible to cut in Linux using a string as the delimiter? cut –delimiter=”delim” -f 1,3 cut reports: cut: the delimiter must be a single character The most closest solution that I find is using awk/gawk: awk -F ‘delim’ ‘{print $1; print $3}’ From the manual: -F fs –field-separator fs Use fs for the…
I have a local svn repository. I work in the repository, e.g. compiling latex documents and building software packages, and there are many useless temporary files there. How can I clean it up by automatically clean these temporary files like the git clean -f in git? svn seems has no built-in function for this. But…
With a list of servers, it is common that one or more are down or crash. Lots cluster management tools can detect the aliveness of servers. However, it can be easily done with ping with a Bash script. I summarize the script that I used and share it here: check-alive-server.sh. Usage: usage: ./check-alive-server.sh file Each…