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Top Forums UNIX for Beginners Questions & Answers How to copy particular files from a multiple directories and paste in a new directory? Post 303042506 by rbatte1 on Friday 27th of December 2019 08:07:27 AM
Old 12-27-2019
Hello dineshkumarsrk,

A few general comments first:-
  • Your for loop has an extra * which might be confusing when you read this later on.
  • It would be better to use longer variable names to make it clear and to reduce the risk of other things that might call this getting confused.
  • The use of backticks ` is deprecated and the way you do it is wasteful too. You add extra processes where the shell can do integer calculations for you.
  • It would be nice to indent your code for clarity
I have made a few tweaks based on these and your code looks like this:-
Code:
count=1
for source_file in */dnaG.fasta
do
   cp "${source_file}" "${count}"_"${source_file}" fastcancatg
   ((count=$count+1))
done

The cp command you have is saying "Copy the source file and the source file again, but with a prefix of the counter and an underscore writing both files to the target directory fastcancatg" which doesn't make sense. The source file with the prefix does not exist. Can I presume that you want to copy the source file to the target directory with a prefix? Perhaps try this instead:-
Code:
count=1
for source_file in */dnaG.fasta
do
   cp "${source_file}" "fastcancatg/${count}"_"${source_file}"
   ((count=$count+1))
done

Is that nearer to what you are after?


Kind regards,
Robin
 

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LN(1)							    BSD General Commands Manual 						     LN(1)

NAME
link, ln -- make links SYNOPSIS
ln [-Ffhinsv] source_file [target_file] ln [-Ffhinsv] source_file ... target_dir link source_file target_file DESCRIPTION
The ln utility creates a new directory entry (linked file) which has the same modes as the original file. It is useful for maintaining mul- tiple copies of a file in many places at once without using up storage for the ``copies''; instead, a link ``points'' to the original copy. There are two types of links; hard links and symbolic links. How a link ``points'' to a file is one of the differences between a hard and symbolic link. The options are as follows: -F If the target file already exists and is a directory, then remove it so that the link may occur. The -F option should be used with either -f or -i options. If none is specified, -f is implied. The -F option is a no-op unless -s option is specified. -h If the target_file or target_dir is a symbolic link, do not follow it. This is most useful with the -f option, to replace a symlink which may point to a directory. -f If the target file already exists, then unlink it so that the link may occur. (The -f option overrides any previous -i options.) -i Cause ln to write a prompt to standard error if the target file exists. If the response from the standard input begins with the char- acter 'y' or 'Y', then unlink the target file so that the link may occur. Otherwise, do not attempt the link. (The -i option over- rides any previous -f options.) -n Same as -h, for compatibility with other ln implementations. -s Create a symbolic link. -v Cause ln to be verbose, showing files as they are processed. By default, ln makes hard links. A hard link to a file is indistinguishable from the original directory entry; any changes to a file are effectively independent of the name used to reference the file. Hard links may not normally refer to directories and may not span file sys- tems. A symbolic link contains the name of the file to which it is linked. The referenced file is used when an open(2) operation is performed on the link. A stat(2) on a symbolic link will return the linked-to file; an lstat(2) must be done to obtain information about the link. The readlink(2) call may be used to read the contents of a symbolic link. Symbolic links may span file systems and may refer to directories. Given one or two arguments, ln creates a link to an existing file source_file. If target_file is given, the link has that name; target_file may also be a directory in which to place the link; otherwise it is placed in the current directory. If only the directory is specified, the link will be made to the last component of source_file. Given more than two arguments, ln makes links in target_dir to all the named source files. The links made will have the same name as the files being linked to. When the utility is called as link, exactly two arguments must be supplied, neither of which may specify a directory. No options may be sup- plied in this simple mode of operation, which performs a link(2) operation using the two passed arguments. COMPATIBILITY
The -h, -i, -n and -v options are non-standard and their use in scripts is not recommended. They are provided solely for compatibility with other ln implementations. The -F option is FreeBSD extention and should not be used in portable scripts. SEE ALSO
link(2), lstat(2), readlink(2), stat(2), symlink(2), symlink(7) STANDARDS
The ln utility conforms to IEEE Std 1003.2-1992 (``POSIX.2''). The simplified link command conforms to Version 2 of the Single UNIX Specification (``SUSv2''). HISTORY
An ln command appeared in Version 1 AT&T UNIX. BSD
February 14, 2006 BSD
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