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Julio
Julio

Posted on • Originally published at jvblog.net on

Quickly exploring CSV files with wc and awk

This week I was extracting high-intensity activity episodes from the Fitbit data of 150 people. The first thing I wanted to know after processing all participants was how many people had at least 1 episode. I am using RAPIDS to process the data, which means that the activity episodes for each participant are stored one per line in CSV files in individual folders. As I was looking for a quick and short solution, I went for Bash instead of Python or R.

Then, the problem is reduced to three steps: list all files in a subfolder with names that match a pattern, count the lines on each file, and filter those files with at least 2 lines (all files have at least the header row). For that, we can use wc and awk.

wc $(find . -name 'p*_fitbit_mvpa_episodes.csv') | awk '{if (($1 > 1) && ($4 ~ /^\.\/data/)) { print }}' | wc -l

The first part wc $(find . -name 'p*_fitbit_mvpa_episodes.csv') executes the wc command on the output of the find command, which retrieves all files in the current directory and any subdirectories with a name that matches the regular expression between quotes. The default output of the wc command has four columns for each file: line count, word count, byte count, and its path. These are piped into awk '{if (($1 > 1) && ($4 ~ /^\.\/data/)) { print }}' which filters and prints those lines where the value of the first column $1 (line count) is bigger than one and the fourth column $4 (file path) starts with ./data. The first part of the filter gets all the files with at least one activity episode (header + episode line), and the second part excludes the total count that wc appends. Finally, to obtain the number of files with at least one activity episode, I piped the previous list to wc with the -l flag that counts the number of lines (files) that awk printed. It turns out that out of 150 participants, only 20 have high-intensity activity episodes (this lead us to discover a problem with the data I was working with that is a matter for another post).

As an extra bit of information useful for our collaborators, I wanted to know the average number of episodes across all participants. For this I followed a similar process but instead of the second wc -l, I piped the output to awk where it is possible to keep a counter and sum of the values of each line, obtaining the average for the first column (line count) as follows:

wc $(find . -name 'p*_fitbit_mvpa_episodes.csv') | awk '{if (($1 > 1) && ($4 ~ /^\.\/data/)) { print $1}}' | awk '{ total += $1; count++ } END { print total/count }'

We have an average of 17.3 episodes across 20 people.

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