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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)								   User Commands							     ln(1)

NAME
ln - make hard or symbolic links to files SYNOPSIS
/usr/bin/ln [-fns] source_file [target] /usr/bin/ln [-fns] source_file... target /usr/xpg4/bin/ln [-fs] source_file [target] /usr/xpg4/bin/ln [-fs] source_file... target DESCRIPTION
In the first synopsis form, the ln utility creates a new directory entry (link) for the file specified by source_file, at the destination path specified by target. If target is not specified, the link is made in the current directory. This first synopsis form is assumed when the final operand does not name an existing directory; if more than two operands are specified and the final is not an existing directory, an error will result. In the second synopsis form, the ln utility creates a new directory entry for each file specified by a source_file operand, at a destina- tion path in the existing directory named by target. The ln utility may be used to create both hard links and symbolic links. A hard link is a pointer to a file and is indistinguishable from the original directory entry. Any changes to a file are effective independent of the name used to reference the file. Hard links may not span file systems and may not refer to directories. ln by default creates hard links. source_file is linked to target. If target is a directory, another file named source_file is created in target and linked to the original source_file. If target is an existing file and the -f option is not specified, ln will write a diagnostic message to standard error, do nothing more with the current source_file, and go on to any remaining source_files. A symbolic link is an indirect pointer to a file; its directory entry contains the name of the file to which it is linked. Symbolic links may span file systems and may refer to directories. File permissions for target may be different from those displayed with an -l listing of the ls(1) command. To display the permissions of target, use ls -lL. See stat(2) for more information. /usr/bin/ln If /usr/bin/ln determines that the mode of target forbids writing, it prints the mode (see chmod(1)), asks for a response, and reads the standard input for one line. If the response is affirmative, the link occurs, if permissible. Otherwise, the command exits. /usr/xpg4/bin/ln When creating a hard link, and the source file is itself a symbolic link, the target will be a hard link to the file referenced by the sym- bolic link, not to the symbolic link object itself (source_file). OPTIONS
The following options are supported for both /usr/bin/ln and /usr/xpg4/bin/ln: -f Links files without questioning the user, even if the mode of target forbids writing. This is the default if the standard input is not a terminal. -s Creates a symbolic link. If the -s option is used with two arguments, target may be an existing directory or a non-existent file. If target already exists and is not a directory, an error is returned. source_file may be any path name and need not exist. If it exists, it may be a file or directory and may reside on a different file system from target. If target is an existing directory, a file is created in directory target whose name is source_file or the last component of source_file. This file is a symbolic link that references source_file. If target does not exist, a file with name target is created and it is a symbolic link that references source_file. If the -s option is used with more than two arguments, target must be an existing directory or an error will be returned. For each source_file, a link is created in target whose name is the last component of source_file. Each new source_file is a symbolic link to the original source_file. The files and target may reside on different file systems. /usr/bin/ln The following option is supported for /usr/bin/ln only: -n If target is an existing file, writes a diagnostic message to stderr and goes on to any remaining source_files. The -f option overrides this option. This is the default behavior for /usr/bin/ln and /usr/xpg4/bin/ln, and is silently ignored. OPERANDS
The following operands are supported: source_file A path name of a file to be linked. This can be either a regular or special file. If the -s option is specified, source_file can also be a directory. target The path name of the new directory entry to be created, or of an existing directory in which the new directory entries are to be created. USAGE
See largefile(5) for the description of the behavior of ln when encountering files greater than or equal to 2 Gbyte ( 2**31 bytes). ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of ln: LANG, LC_ALL, LC_CTYPE, LC_MES- SAGES, and NLSPATH. EXIT STATUS
The following exit values are returned: 0 All the specified files were linked successfully >0 An error occurred. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: /usr/bin/ln +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWcsu | +-----------------------------+-----------------------------+ |CSI |Enabled | +-----------------------------+-----------------------------+ /usr/xpg4/bin/ln +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWxcu4 | +-----------------------------+-----------------------------+ |CSI |Enabled | +-----------------------------+-----------------------------+ |Interface Stability |Standard | +-----------------------------+-----------------------------+ SEE ALSO
chmod(1), ls(1), stat(2), attributes(5), environ(5), largefile(5), standards(5) NOTES
A symbolic link to a directory behaves differently than you might expect in certain cases. While an ls(1) command on such a link displays the files in the pointed-to directory, entering ls -l displays information about the link itself: example% ln -s dir link example% ls link file1 file2 file3 file4 example% ls -l link lrwxrwxrwx 1 user 7 Jan 11 23:27 link -> dir When you change to a directory (see cd(1)) through a symbolic link, using /usr/bin/sh or /usr/bin/csh, you wind up in the pointed-to loca- tion within the file system. This means that the parent of the new working directory is not the parent of the symbolic link, but rather, the parent of the pointed-to directory. This will also happen when using cd with the -P option from /usr/bin/ksh or /usr/xpg4/bin/sh. For instance, in the following case, the final working directory is /usr and not /home/user/linktest. example% pwd /home/user/linktest example% ln -s /usr/tmp symlink example% cd symlink example% cd .. example% pwd /usr C shell users can avoid any resulting navigation problems by using the pushd and popd built-in commands instead of cd. SunOS 5.10 25 Mar 2004 ln(1)
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