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Full Discussion: Problem with File Names under tcsh loop
Top Forums Shell Programming and Scripting Problem with File Names under tcsh loop Post 302465452 by InfoSeeker on Friday 22nd of October 2010 12:28:37 PM
Old 10-22-2010
Question Problem with File Names under tcsh loop
Hello,
I have a question regarding file naming under a loop in tcsh. I have the following code:
Code:
#!/bin/tcsh
foreach file (test/ProteinDirectory/*)   # The * is a bunch of ProteinFile1, ProteinFile2, ProteinFile3, etc.
sh /bioinfo/home/dgendoo/THREADER/pGenThreader.sh $file $file 
         #the first $file is really supposed to represent the filename, the second $file is the actual path!
echo DONE! $file#protein name is what I'm aiming for
end

The problem:
If I echo $file in the loop, it will print the entire path: test/ProteinDirectory/ProteinFile1
I want a way to only extract the actual file name (ex: ProteinFile1) to use in the loop to rename my files, and still retain the $file because I need that path as input.
So in that case the code would be something like:

Code:
#!/bin/tcsh
foreach file (test/ProteinDirectory/*)
set ProteinName = ?? 
           # Where ProteinName = ProteinFile1, ProteinFile2, etc. Probably some string manipulation on $file
sh /bioinfo/home/dgendoo/THREADER/pGenThreader.sh ProteinName $file
echo DONE! ProteinName
end

1. Could you suggest a way to do this? I think it could be done in Sed with a / delimiter, but I am not very familiar with that language.

2. I also wanted to try and modify this loop so that I only work on 200 ProteinFiles at one time, so I wanted some sort of condition to say "execute from ProteinFile5 to ProteinFile205". I would really appreciate some input on how to incorporate this condition into the loop also.

Thank you very much for your help!
Last edited by vbe; 10-22-2010 at 01:48 PM.. Reason: Code tags please
 

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LEARN ABOUT SUNOS

shells

shells(4)							   File Formats 							 shells(4)

NAME

       shells - shell database

SYNOPSIS

       /etc/shells

DESCRIPTION

       The shells file contains a list of the shells on the system. Applications use this file to determine whether a shell is valid. See getuser-
       shell(3C). For each shell a single line should be present, consisting of the shell's path, relative to root.

       A hash mark (#) indicates the beginning of a comment; subsequent characters up to the end of the line are not interpreted by  the  routines
       which search the file. Blank lines are also ignored.

       The  following  default	shells are used by utilities: /bin/bash, /bin/csh, /bin/jsh, /bin/ksh, /bin/pfcsh, /bin/pfksh, /bin/pfsh, /bin/sh,
       /bin/tcsh,  /bin/zsh,  /sbin/jsh,  /sbin/sh,  /usr/bin/bash,  /usr/bin/csh,  /usr/bin/jsh,  /usr/bin/ksh,  /usr/bin/pfcsh,  /usr/bin/pfksh,
       /usr/bin/pfsh, and /usr/bin/sh, /usr/bin/tcsh, /usr/bin/zsh. Note that /etc/shells overrides the default list.

       Invalid shells in /etc/shells may cause unexpected behavior (such as being unable to log in by way of ftp(1)).

FILES

       /etc/shells	       lists shells on system

SEE ALSO

       vipw(1B), ftpd(1M), sendmail(1M), getusershell(3C), aliases(4)

SunOS 5.10							    4 Jun 2001								 shells(4)
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