08-07-2014
You have told us a lot about which lines were messing up, but what's less clear is what you'd want the program to be doing, if it were working.
Quote:
Originally Posted by
hmortens
Problem 1: I currently have stout sent to a file (stout.miRNA.bash.$date_formatted) which I would like to have work inside my loop, but when I move it, it just prints to the screen.
Both cases do what I'd expect them to do.. What were you expecting?
Quote:
Problem 2: I have a second file (summary.fastqc.$date_formatted), which is basically redirecting the same output file from multiple run output directories.
Is there a way to consolidate these output within the loop so that there is no need for the last cat statement (which is not working) and a third file? So, the script would basically print stout1 summary1; stout2 summary2;... stoutN summaryN.
What do you mean by "redirect" here?
What are stout1 summary1, stout2 summary2, ...?
In what way is the cat "not working"?
Quote:
Problem 3: Is there a way to add in sed/awk to print out specific lines (using search term) of the stout (stout.miRNA.bash.$date_formatted) within the loop, so that I could get the mother load and have edited_stout1 summary1; edited_stout2 summary2;... edited_stoutN summaryN?
Probably, once we know what files you're talking about and what you want us to do to them.
Quote:
...seems to only be stout.miRNA.bash that is being written.
Check the contents of 'summary' then, if they don't appear in the output they probably weren't there in the first place.
Last edited by Corona688; 08-07-2014 at 06:37 PM..
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LEARN ABOUT DEBIAN
continue
continue(3tcl) Tcl Built-In Commands continue(3tcl)
__________________________________________________________________________________________________________________________________________________
NAME
continue - Skip to the next iteration of a loop
SYNOPSIS
continue
_________________________________________________________________
DESCRIPTION
This command is typically invoked inside the body of a looping command such as for or foreach or while. It returns a TCL_CONTINUE code,
which causes a continue exception to occur. The exception causes the current script to be aborted out to the innermost containing loop
command, which then continues with the next iteration of the loop. Catch exceptions are also handled in a few other situations, such as
the catch command and the outermost scripts of procedure bodies.
EXAMPLE
Print a line for each of the integers from 0 to 10 except 5:
for {set x 0} {$x<10} {incr x} {
if {$x == 5} {
continue
}
puts "x is $x"
}
SEE ALSO
break(3tcl), for(3tcl), foreach(3tcl), return(3tcl), while(3tcl)
KEYWORDS
continue, iteration, loop
Tcl continue(3tcl)