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Full Discussion: Redirecting stdout inside a loop
Top Forums UNIX for Dummies Questions & Answers Redirecting stdout inside a loop Post 302912750 by hmortens on Monday 11th of August 2014 04:34:22 PM
Old 08-11-2014
Quote:
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.
is it possible to organize it real time? like as it is being written to file?

Here is the code for CutAdapt, where the /Processed reads/ and /Trimmed reads/ come from:
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

Here is the call to sRNAbench where the other bits come from.
Code:
#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

I was not specific about this before because I thought it would be the same pattern search, but I need to pull lines containing "No. input reads:", "No. reads in analysis:", "mapped...reads to genomes(s)", and "Detected:" The stdout for that portion looks like this:
Code:
           START WITH THE PRE-PROCESSING OF THE READS             

               Reading file: /illumina/runs/Runs/140513_H207_0249_AD2B9LACXX/Unaligned_Lane1/Project_DefaultProject/Sample_GRC270_DEHP2_67C/GRC270_DEHP2_67C_cutadapt_AdapterRemoved.fastq.gz

             Result of pre-processing

               No. input reads: 2139267
               No. cleaned input reads (adapter found and trimmed): 0
               No. input reads where the adapter was not found: 2139267
               No. length filtered input reads (min. Length): 192482
               No. length filtered input reads (max. Length): 0
               No. reads in analysis: 1570818
               No. unique reads in analysis: 78295
               Max. read length in analysis: 51
               Filtered reads (low quality or low read count): 375967
               Max. read length in input file: 51

           FINISHED PRE-PROCESSING

I have already shown you the summary.txt file.
The call to that program is
#run QC with FastQC
#/illumina/runs/Runs/FastQC/fastqc --outdir=$LOCATION --quiet $infile2
 

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LEARN ABOUT DEBIAN

fst-infl

fst-infl(1)							     fst-infl							       fst-infl(1)

NAME

       fst-infl - morphological analysers

SYNOPSIS

       fst-infl [ options ] file [ input-file [ output-file ] ]
       fst-infl2 [ options ] file [ input-file [ output-file ] ]
       fst-infl3 [ options ] file [ input-file [ output-file ] ]

OPTIONS

       -t file
	      Read  an	alternative  transducer from file and use it if the main transducer fails to find an analysis. By iterating this option, a
	      cascade of transducers may be tried to find an analysis.

       -b     Print surface and analysis symbols. (fst-infl2 only)

       -n     Print multi-character symbols without the enclosing angle brackets.  (fst-infl only)

       -d     The analyses are symbolically disambiguated by returning only analyses with a minimal number of morphemes. This option requires that
	      morpheme	boundaries are marked with the tag <X>. If no <X> tag is found in the analysis string, then the program (basically) counts
	      the number of multi-character symbols consisting entirely of upper-case characters and uses this count for disambiguation. The  lat-
	      ter heuristic was developed for the German SMOR morphology. (This option is only available with fst-infl2 and fst-infl3.)

       -e n   If  no  regular  analysis  is found, do robust matching and print analyses with up to n edit errors. The set of edit operations cur-
	      rently includes replacement, insertion and deletion. Each operation has currently a fixed error weight of 1. (fst-infl2 only)

       -% f   Disambiguates the analyses statistically and prints the most likely analyses with at least f % of the total probability mass of  the
	      analyses.  The  transducer  weights  are read from a file obtained by appending .prob to the name of the transducer file. The weight
	      files are created with fst-train.  (fst-infl2 only)

       -p     Print the probability of each analysis. (fst-infl2 only)

       -c     use this option if the transducer was compiled on a computer with a different endianness. If you have a transducer  which  was  com-
	      piled on a Sparc computer and you want to use it on a Pentium, you need to use this option. (fst-infl2 only)

       -q     Suppress status messages.

       -h     Print usage information.

DESCRIPTION

       fst-infl is a morphological analyser. The first argument is the name of a file which was generated by fst-compiler.  The second argument is
       the name of the input file. The third argument is the output file. If the third argument is missing, output is directed to stdout.  If  the
       second argument is missing, as well, input is read from stdin.

       fst-infl2  is  similar to fst-infl but needs a transducer in compact format (see the man pages for fst-compiler and fst-compact). fst-infl2
       is implemented differently from fst-infl and usually much faster.

       fst-infl3 is also similar to fst-infl but needs a transducer in lowmem format (see the man pages for  fst-compiler  and	fst-lowmem).  fst-
       infl3  accesses	the transducer on disc rather than reading it into memory. It starts very fast and needs very little memory, but is slower
       than fst-infl2.

       fst-infl reads the transducer which is stored in the argument file. Then it reads the input file line by line. Each line is  analysed  with
       the transducer and all resulting analyses are printed (see also the man pages for fst-mor).

BUGS

       No bugs are known so far.

SEE ALSO

       fst-compiler, fst-mor

AUTHOR

       Helmut  Schmid,	Institute  for	Computational  Linguistics,  University of Stuttgart, Email: schmid@ims.uni-stuttgart.de, This software is
       available under the GNU Public License.

								   November 2004						       fst-infl(1)
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