Gesquiere2011_pseudo.md

Hints and pseudo code for Exercise 1.10.2 (data from Gesquiere et al., 2011)

1. You can use cut to extract just the maleID from the file; to match the individual 3 (or 27), you can use grep.
2. You want to turn the solution of part 1 into a script; to do so, open a new file and copy the code you've written. Now you can use generic variables $1 and $2 as placeholders for the file name and the maleID; you can pass these arguments to the command line.
3. First, you need to use cut in combination with tail, sort and uniq to extract all the distinct maleID. Then the main hurdle is to take the output of this pipeline and use it as input for a for loop in bash. The following example should help:

#!/bin/bash

# to store the results of a command into a variable,
# surround the command with backticks (`)
myfiles=`ls`
for myfile in $myIDS
do
    echo $myfile
done