Moving files to directories based on part of filename

[fritzonline]

I have a single directory of pairs of files, with the pairs sharing a string as the beginning of the filename:

SF1-27F1492R-clone01_T3_A18_001.ab1
SF1-27F1492R-clone01_T7_A20_002.ab1
SF1-27F1492R-clone02_T3_A19_003.ab1
SF1-27F1492R-clone02_T7_A21_004.ab1
...etc

I need to create a subdirectory for each pair then move the pair into the subdirectory.

I accomplished the first step using:

$find /foo -name '*T3*' -exec mkdir '{}.wrk' \;

I can use a regex to designate the pair and associate the directory, but how do I use regex in a path as the output of a move command?

[Lakshmipathi]

Could you please explain with some example --step by step ,if possible

[fritzonline]

Could you please explain with some example --step by step ,if possible

I'll detail what I need first, then how I achieved it.

1. Create directories (with a subdirectory structure from a template directory) based on the first common part of two filenames. So from this list:

SF1-27F1492R-clone01_T3_A18_001.ab1
SF1-27F1492R-clone01_T7_A20_002.ab1
SF1-27F1492R-clone02_T3_A22_003.ab1
SF1-27F1492R-clone02_T7_A24_004.ab1
SF1-27F1492R-clone03_T3_A26_005.ab1
SF1-27F1492R-clone03_T7_A28_006.ab1

Create the directories:

SF1-27F1492R-clone01
SF1-27F1492R-clone02
SF1-27F1492R-clone03

2. Move each pair of files into the corresponding directory (within a subdirectory).

So
SF1-27F1492R-clone01_T3_A18_001.ab1
SF1-27F1492R-clone01_T7_A20_002.ab1

are both moved into

SF1-27F1492R-clone01/edit_dir/

etc.

[fritzonline]

This is how I achieved it (with my logic)

1. $ rename 's/\_T3\w{8}/-T3/' *
(I don't need the end of the filename)

2. $ find /home/foo/assembly -type f -name '*T3*' -exec cp -a /home/foo/template '{}.wrk' \;
(To make one directory for each pair of files)

3. $find /home/foo/assembly -type f -name '*T3*' -exec mv '{}' '{}.wrk/edit_dir/' \;
(Move one file from each pair into the directory)

4. $ rename 's/\_T7\w{8}/-T7/' *
(Same logic as 1.)

5. $ rename 's/-T3/-T7/' *
(Renames the directory to match the remaining file)

6. $ find /home/foo/assembly -type f -name '*T7*' -exec mv '{}' '{}.wrk/edit_dir/' \;
(Moves the remaining file of the pair into the directory)

7. $ rename 's/-T7.ab1.wrk//' *
(Renames the directory to be the prefix of the two files)

The outcome:

$ ls SF1-27F1492R-clone01/edit_dir/
SF1-27F1492R-clone01-T3.ab1 SF1-27F1492R-clone01-T7.ab1

[Lakshmipathi]

ls  | cut -f1 -d'T' > uniq.txt
uniq uniq.txt  > create_dir.txt
while read line; do mkdir $line; done < create_dir.txt

This should give you directories like
SF1-27F1492R-clone01_
SF1-27F1492R-clone02_
SF1-27F1492R-clone03_

then do

while read line; do mv $line*.ab1 $line; done < create_dir.txt

to move files into their directories.

HTH

[fritzonline]

My method works, but it felt clumsy because I had to manipulate the name of the directory to match the name of the first file, then add a suffix to the directory, then manipulate the directory name again for the second file.

Basically, I couldn't use find to mv both files together because find -exec {} didn't allow me to use part of the filename (in this case SF1-27F1492R-clone01) as the output of the mv command.

In essence, is there an alternative to:

$find /foo -type f * -exec mv '{}' '{}.suffix/edit_dir' \;

that will allow me to move the files to a directory with a smaller name than the filenames, but with a common prefix ie move files foo1.suffix foo2.suffix foo3.suffix to directory foo.

[fritzonline]

Thanks, with a few changes (to cp a template directory instead of mkdir and then mv files into a subdirectory) your method works great.

[Lakshmipathi]

In essence, is there an alternative to:

$find /foo -type f * -exec mv '{}' '{}.suffix/edit_dir' \;

As of now , I can't think of an alternative ! I think about it and get back here