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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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while(n)						       Tcl Built-In Commands							  while(n)

__________________________________________________________________________________________________________________________________________________

NAME
while - Execute script repeatedly as long as a condition is met SYNOPSIS
while test body _________________________________________________________________ DESCRIPTION
The while command evaluates test as an expression (in the same way that expr evaluates its argument). The value of the expression must a proper boolean value; if it is a true value then body is executed by passing it to the Tcl interpreter. Once body has been executed then test is evaluated again, and the process repeats until eventually test evaluates to a false boolean value. Continue commands may be exe- cuted inside body to terminate the current iteration of the loop, and break commands may be executed inside body to cause immediate termi- nation of the while command. The while command always returns an empty string. Note: test should almost always be enclosed in braces. If not, variable substitutions will be made before the while command starts execut- ing, which means that variable changes made by the loop body will not be considered in the expression. This is likely to result in an infinite loop. If test is enclosed in braces, variable substitutions are delayed until the expression is evaluated (before each loop iter- ation), so changes in the variables will be visible. For an example, try the following script with and without the braces around $x<10: set x 0 while {$x<10} { puts "x is $x" incr x } EXAMPLE
Read lines from a channel until we get to the end of the stream, and print them out with a line-number prepended: set lineCount 0 while {[gets $chan line] >= 0} { puts "[incr lineCount]: $line" } SEE ALSO
break(n), continue(n), for(n), foreach(n) KEYWORDS
boolean value, loop, test, while Tcl while(n)
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