08-11-2014
Quote:
Originally Posted by
hmortens
Ah. The file stout.miRNA.bash.$date_formatted is capturing the stdout from all three programs. I am trying to extract lines from the Cutadapt stdout and the sRNAbench stdout here.
Great. Which is which? What do they look like individually? What do you want from each individually?
You have to organize it
before it gets dumped into the same giant pile, not after, so we need to alter their output, not edit the great giant file, I think.
Quote:
This is actually a folder (containing the actual data being processed).
Great. What files are in it that I need to worry about?
Is the fastqc
inside the Sample, then?
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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)