Friday, April 23, 2010

reordering columns in a text grid

I just wanted to quickly move a column around in a grid file (tab separated text data file), and had to look up a few commands to do it.

cut - I use this program quite often to select columns from a grid.

paste - join two files line by line with corresponding lines separated with a tab.

paste <(cut -d $'\t' -f 3 $file) <(cut -d $'\t' -f 1,2,4,5,6 $file) | sort > $out

Basically the two cuts run in parallel, and are piped into paste which reads each a line at a time and outputs the pasted lines, the rest of the command line just sorts the result and saves it to a file.

I am doing this to try and do a binary search on the text file.

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