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Full Discussion: Syntax error near unexpected token `('
Top Forums Shell Programming and Scripting Syntax error near unexpected token `(' Post 302391968 by hergp on Wednesday 3rd of February 2010 03:06:45 AM
Old 02-03-2010
You just rename $OUTFILE to $OUTFILE$(date +%y%m%d-%H%M%S).${DPDEVICE}, so ${OUTFILE} does no longer exist when to try to change it's access mode. You have to save the new name in a variable for later use, because 'date' might give a different timestamp when you rerun 'date'.

Code:
NEWFILE=$OUTFILE$(date +%y%m%d-%H%M%S).${DPDEVICE}
mv -if $OUTFILE $NEWFILE
...
chmod 755 $NEWFILE

To display a certain line from the outfile, you can use 'grep' or 'awk' for example.

---------- Post updated at 09:06 ---------- Previous update was at 09:03 ----------

Just recongnized, that NEWFILE does not get set in the else-part just before the chmod. So you have to set NEWFILE=$OUTFILE in the else-part or - if it is OK to run 'chmod' only in the then-block - move 'chmod' just before the 'mv' command:

Code:
chmod 755 $OUTFILE
mv -if $OUTFILE $OUTFILE$(date +%y%m%d-%H%M%S).${DPDEVICE}

 

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LEARN ABOUT DEBIAN

fastq_quality_trimmer

FASTQ_QUALITY_TRIMMER(1)					   User Commands					  FASTQ_QUALITY_TRIMMER(1)

NAME

       fastq_quality_trimmer - Filters sequences based on quality

DESCRIPTION

       usage:  fastq_quality_trimmer  [-h]  [-v]  [-t  N]  [-l	N] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13.1 by A. Gordon (gor-
       don@cshl.edu)

       [-h]   = This helpful help screen.

       [-t N] = Quality threshold - nucleotides with lower

	      quality will be trimmed (from the end of the sequence).

       [-l N] = Minimum length - sequences shorter than this (after trimming)

	      will be discarded. Default = 0 = no minimum length.

       [-z]   = Compress output with GZIP.

       [-i INFILE]
	      = FASTQ input file. default is STDIN.

	      [-o OUTFILE] = FASTQ output file. default is STDOUT.  [-v]	 = Verbose - report number of sequences.

       If [-o] is specified,
	      report will be printed to STDOUT.

	      If [-o] is not specified (and output goes to STDOUT), report will be printed to STDERR.

SEE ALSO

       The quality of this automatically generated manpage might be insufficient.  It is suggested to visit

	      http://hannonlab.cshl.edu/fastx_toolkit/commandline.html

       to get a better layout as well as an overview about connected FASTX tools.

fastq_quality_trimmer 0.0.13.1					    April 2012						  FASTQ_QUALITY_TRIMMER(1)
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