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Full Discussion: awk script to find min and max value
Top Forums Shell Programming and Scripting awk script to find min and max value Post 302904801 by ncwxpanther on Friday 6th of June 2014 02:28:34 PM
Old 06-06-2014
awk script to find min and max value
I need to find the max/min of columns 1 and 2 of a 2 column file what contains the special character ">".

I know that this will find the max value of column 1.
Code:
awk 'BEGIN {max = 0} {if ($1>max) max=$1} END {print max}' input.file

But what if I needed to ignore special characters in the file. How would I put in that exception?
 

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LEARN ABOUT DEBIAN

fastx_quality_stats

FASTX_QUALITY_STATS(1)						   User Commands					    FASTX_QUALITY_STATS(1)

NAME

       fastx_quality_stats - FASTX Statistics

DESCRIPTION

       usage: fastx_quality_stats [-h] [-N] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13.2 by A. Gordon (gordon@cshl.edu)

	      [-h]  =  This  helpful help screen.  [-i INFILE]	= FASTQ input file. default is STDIN.  [-o OUTFILE] = TEXT output file. default is
	      STDOUT.  [-N]	    = New output format (with more information per nucleotide/cycle).

   The *OLD* output TEXT file will have the following fields (one row per column):
       column = column number (1 to 36 for a 36-cycles read solexa file)

       count  = number of bases found in this column.

       min    = Lowest quality score value found in this column.

       max    = Highest quality score value found in this column.

       sum    = Sum of quality score values for this column.

       mean   = Mean quality score value for this column.

       Q1     = 1st quartile quality score.

       med    = Median quality score.

       Q3     = 3rd quartile quality score.

       IQR    = Inter-Quartile range (Q3-Q1).

       lW     = 'Left-Whisker' value (for boxplotting).

       rW     = 'Right-Whisker' value (for boxplotting).

	      A_Count = Count of 'A' nucleotides found in this column.	C_Count = Count of 'C' nucleotides found in this column.  G_Count =  Count
	      of  'G'  nucleotides found in this column.  T_Count = Count of 'T' nucleotides found in this column.  N_Count = Count of 'N' nucleo-
	      tides found in this column.  max-count = max. number of bases (in all cycles)

   The *NEW* output format:
	      cycle (previously called 'column') = cycle number max-count For each nucleotide in the cycle (ALL/A/C/G/T/N):

       count  = number of bases found in this column.

       min    = Lowest quality score value found in this column.

       max    = Highest quality score value found in this column.

       sum    = Sum of quality score values for this column.

       mean   = Mean quality score value for this column.

       Q1     = 1st quartile quality score.

       med    = Median quality score.

       Q3     = 3rd quartile quality score.

       IQR    = Inter-Quartile range (Q3-Q1).

       lW     = 'Left-Whisker' value (for boxplotting).

       rW     = 'Right-Whisker' value (for boxplotting).

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.

fastx_quality_stats 0.0.13.2					     May 2012						    FASTX_QUALITY_STATS(1)
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