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I am new to shell scripting so apologies if this was asked before.

I have a file coordinates.txt like this:

765442
866447
755343
097754

I would like to pass each value of each line of the file to a variable and use those values one by one as input in a command line and save that number in part of the file name. I wrote the following code but not sure if this is the correct way to go...

cat coordinates.txt | while read LINE; do
    var="$(echo $LINE)"
    /home/users/scripts/TreeView/TreeView.sh -o $NAME_ALL.chr1.new_estimate.trees.$var --bp_of_interest $var
done

so in the output -o each value one at the time is appended to the file name and each value is also used as --bp_of_interest, one at the time

Any suggestion highly appreciated. Thanks

Paolo Lorenzini
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    What is $NAME_ALL? You need to double quote all variable expansions, and var="$(echo $LINE)" is better written var="$LINE". Also, remove that cat and redirect the file into the loop with while read ...; done <coordinates.txt. – Kusalananda Jul 23 '19 at 16:15
  • $NAME_ALL is another variable of the beginning of the file name which is already in my environment, it is different from the variables (var) from the file – Paolo Lorenzini Jul 23 '19 at 16:18
  • sure, thanks for the suggestion – Paolo Lorenzini Jul 23 '19 at 16:19
  • something like this?: while read LINE; do var="$LINE" /home/users/scripts/TreeView/TreeView.sh -o $NAME_ALL.chr1.new_estimate.trees."$var" --bp_of_interest "$var" done <coordinates.txt – Paolo Lorenzini Jul 23 '19 at 16:22
  • it is working very well, wonderfull – Paolo Lorenzini Jul 23 '19 at 16:30

1 Answers1

2

Your loop is better written as

PATH=/home/users/scripts/TreeView:$PATH

while IFS= read -r line; do
    TreeView.sh -o "$name_all.chr1.new_estimate.trees.$line" --bp_of_interest "$line"
done <coordinates.txt

This changes the following:

  • I added /home/users/scripts/TreeView to the front of $PATH. This allows us to call TreeView.sh without the absolute path prepended to it.
  • I deleted the var variable, as it was just the same as the value read from the input file.
  • I use IFS= read -r line because "Understanding "IFS= read -r line"".
  • I used lower-case variable names because "Are there naming conventions for variables in shell scripts?".
  • I pass the data from the file into the loop with a redirection, because using cat in this instance is just not needed.

Another way to do the same thing:

PATH=/home/users/scripts/TreeView:$PATH

xargs -I {} TreeView.sh -o "$name_all.chr1.new_estimate.trees.{}" --bp_of_interest "{}" <coordinates.txt

This uses xargs to insert the data read from each line of coordinates.txt into the arguments of the TreeView.sh script in the locations denoted by {}.

You could even add -P n to the xargs command line (e.g. before -I {}, where n is some number) to run that many parallel instances of the script at once, each with the appropriate data inserted into its command line from coordinates.txt.

Kusalananda
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