https://divingintogeneticsandgenomics.com/tags/sort/ Recent content in Sort on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Thu, 29 Oct 2015 12:35:00 -0700 https://divingintogeneticsandgenomics.com/archive/merge-the-sub-cytobands-to-major-cytoband-and-get-the-coordinates/ Thu, 29 Oct 2015 12:35:00 -0700 https://divingintogeneticsandgenomics.com/archive/merge-the-sub-cytobands-to-major-cytoband-and-get-the-coordinates/ In my pervious blog post, I wrote How to get the cooridnates of the cytobands Now, how about I want to get coordinates of the bigger band merging all the sub-bands. ex. chr1 p36.33 p36.32, p36.31, p36.23, p36.22, p36.13, p36.12, p36.11....p31.1 to p3 chr1 0 84900000 This is a task that requires some efforts for text processing. First look at what the data look like: head -30 cytoBand.txt chr1 0 2300000 p36. https://divingintogeneticsandgenomics.com/archive/sort-with-header-maintained/ Tue, 25 Aug 2015 13:36:00 -0700 https://divingintogeneticsandgenomics.com/archive/sort-with-header-maintained/ We usually want to maintain header when we do something for the body of the text. You can find a body function here which can only accept streams and assumes only one line header. Use subshells and awk can do the same job and potentially more flexible. View this gist on GitHub The original credits go to Aaron Quinlan. see a gist below to sort vcf files in natural chromosome order :chr1 chr2 chr3. https://divingintogeneticsandgenomics.com/archive/unix-sort-except-the-first-line/ Mon, 03 Mar 2014 11:49:00 -0800 https://divingintogeneticsandgenomics.com/archive/unix-sort-except-the-first-line/ Many times I have a file with a header needs to be sorted, but I do not want to sort the header. I saw it on Twitter:  Retweeted by Ming Tang razor ‏@razZ0r  Mar 1 todays fav linux oneliner: command | (read -r; printf "%s\n" "$REPLY"; sort) > output sort everything except first line. REPLY is the default variable for the read command. one more general use of the "body" function