Redirecting stdout inside a loop Post: 302912743

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Top Forums UNIX for Dummies Questions & Answers Redirecting stdout inside a loop Post 302912743 by hmortens on Monday 11th of August 2014 04:13:47 PM

08-11-2014

Registered User

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. The fastQC is writing the summary.txt.

Code:

#run CutAdapt to trim Wafergen adapter 
/usr/local/bin/python2.7 /illumina/runs/Runs/cutadapt-1.2.1/bin/cutadapt -a AGATCGGAAGAGCACACGTCT -o $i/${y#*/Sample_*}_cutadapt_AdapterRemoved.fastq.gz $infile 

#define cutadapt output as infile2  
	infile2=`ls $i/*cutadapt_AdapterRemoved.fastq.gz`
	echo "**testing**" $infile2

#run QC with FastQC
/illumina/runs/Runs/FastQC/fastqc --outdir=$LOCATION --quiet $infile2

#run sRNAbench w/o adapter trimming
java -jar /illumina/runs/Runs/miRanalyzer/sRNAbenchDB/sRNAbench.jar input=$infile2 output=${y#*/Sample_*}.sRNAbench.$date_formatted dbPath=/illumina/runs/Runs/miRanalyzer/sRNAbenchDB/ species=$speciesBuild microRNA=$speciesAbbrev p=14 noMM=0 alignType=v minRC=2

Quote:

"$LOCATION"/Sample_* matches all sample files (not folders).

This is actually a folder (containing the actual data being processed).

Quote:

What exactly do these paths / filenames have in common? You can't use * to match one and * to match the other when you want pairs, since they both expand to complete lists. Do you find the sample in Sample_abcde, and the summary in abcde_fastqc ?

The Location is the Project (a folder with many sample data folders); The Sample_* is the data folder for each sample; the *_fastqc is the output folder for each sample from one program, fastqc, where each folder contains a summary.txt.

thank you for taking the time. I really appreciate your help.

hmortens

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LEARN ABOUT OPENSOLARIS

continue

continue(1T)						       Tcl Built-In Commands						      continue(1T)

__________________________________________________________________________________________________________________________________________________

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(1T), for(1T), foreach(1T), return(1T), while(1T)

KEYWORDS

       continue, iteration, loop

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +--------------------+-----------------+
       |  ATTRIBUTE TYPE    | ATTRIBUTE VALUE |
       +--------------------+-----------------+
       |Availability	    | SUNWTcl	      |
       +--------------------+-----------------+
       |Interface Stability | Uncommitted     |
       +--------------------+-----------------+
NOTES

       Source for Tcl is available on http://opensolaris.org.

Tcl																      continue(1T)