mjhjmtu

This script copies all the files to all the folders. But I am struggling to construct a condition statement that will specify to which folder each file is copied to. I've tried the if statement but no copy is made at all.

The reason I use parameter expansion is because the file names are like, Long_John_Silver, Miss_Havisham and Master_Pip and the folder names are like Long, Miss and Master. So essentially I'm trying to copy the files to their respective folders e.g. Master_Pip.fna.gz into the folder named Master. And so what I've tried to do is to capture the first word of the file name and somehow use that as a reference.

for fldr in /home/scripts/playground/genomes_2/* ; do
 find . -name *fna.gz | while read f ; do
 basenm=$fldr##*/ ; f_name=$basenm%%_* ; 
 cp -r $f /home/scripts/playground/port/$f_name/ ;
 done
done

This is my script with the if statement, but this script copies nothing at all.

for fldr in /home/scripts/playground/genomes_2/* ; do
 find . -name *fna.gz | while read f ; do
 basenm=$fldr##*/ ; f_name=$basenm%%_* ; 
 if [ "$f_name" == /home/scripts/playground/port/"$f_name" ] ; then
 cp -r $f /home/scripts/playground/port/"$f_name"/ ;
 else
 continue 
 fi
 done
done

1.
Change this code

basenm=$fldr##*/;

to this one

basenm=$f##*/ ;

and remove -r switch from copy command

cp $f /home/scripts/playground/port/"$f_name"

Maybe you have some jumbled source paths like this /home/scripts/playground/genomes_2/Long_John_Silver/Master_Pip.fna.gz. So, when you're extracting f_name from folder name fldr you get 'Long'. Then you copy Master_Pip.fna.gz to the ..../Long folder.
2.

"$f_name" == /home/scripts/playground/port/"$f_name"

they are not equal, and they won't.

Basically, your first script is good. Condition is redundant because you do it implicitly by parameter expansion.

I would only add directory creation command before copying. So you'll always have a directory to copy to in case new person appears in source directory, Shorty_Pete for example.

mkdir -p /home/scripts/playground/port/"$f_name"
cp ...

I realised that I was copying all the files into all the folders based on the type of file i.e. .fna.gz, so I specified what type of fna.gz file I want to be read and then copied. There is no need for an if statement since the specificity is implied through the parameter expansion. It now works perfectly.

for fldr in /home/scripts/playground/genomes_2/* ; do

basenm=$fldr##*/ ; f_name=$basenm%%_* ; 

find . -name $f_name*fna.gz | while read f ; do

 cp -r $f /home/scripts/playground/port/$f_name/ ;



done

done