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Full Discussion: A mistake in awk command I used to parse numbers
Top Forums Shell Programming and Scripting A mistake in awk command I used to parse numbers Post 302498190 by Lucky Ali on Sunday 20th of February 2011 10:11:54 AM
Old 02-20-2011
A mistake in awk command I used to parse numbers
Hi

I have a big file with a certain pattern (shown below) from which I need to parse out some digits in tabular format.

The format of the file is: '-' indicates text which doesn't to be parsed
Code:
# Output of huzzle for sequence file 1000.Clade1.html
  - - - -- ------- -----------------------------------------
  ---------------------------------------------------------
 ------------------------------------------------------------
 ---------------------------------------------------------------
# SCORE     7.951      0.6909        -0.32       0.0026   
  ------------------------------------------------------------
 -------------------------------------------------------------
----------------------------------------------------------------
# Output of huzzle for sequence file 1001.Clade1.html
  - - - -- ------- -----------------------------------------
  ---------------------------------------------------------
 ------------------------------------------------------------
 ---------------------------------------------------------------
# SCORE     7.951      0.0909        -0.32       0.0026   
  ------------------------------------------------------------
 -------------------------------------------------------------
----------------------------------------------------------------
# Output of huzzle for sequence file 1002.Clade1.html
  - - - -- ------- -----------------------------------------
  ---------------------------------------------------------
 ------------------------------------------------------------
 ---------------------------------------------------------------
# SCORE     7.951      0.07909        -0.32       0.0026   
  ------------------------------------------------------------
 -------------------------------------------------------------
----------------------------------------------------------------
# Output of huzzle for sequence file 1003.Clade1.html
  - - - -- ------- -----------------------------------------
  ---------------------------------------------------------
 ------------------------------------------------------------
 ---------------------------------------------------------------
# SCORE     7.951      0.0109        -0.32       0.0026   
  ------------------------------------------------------------
 -------------------------------------------------------------
----------------------------------------------------------------



What numbers I need to parse out is; for example the 1003 from "Output of huzzle for sequence file 1003.Clade1.html" and 0.0109 from "SCORE 7.951 0.0109 -0.32 0.0026"..like wise from all those patterns

So that I would get the tab delimited file as:
Code:
1000 0.6909
1001 0.0909
1002 0.07909
1003 0.0109

I tried with the following awk code but I am not getting it correctly
Code:
awk '
/^Output of huzzle for sequence file/ {r1=$7;gsub(/\..*/,"",r1)}
/^SCORE/ {r2=$2;print r1,r2}' my file

Please let me know what might be the error.

LA
 

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LEARN ABOUT DEBIAN

fasta_formatter

FASTA_FORMATTER(1)						   User Commands						FASTA_FORMATTER(1)

NAME

       fasta_formatter - changes the width of sequences line in a FASTA file

DESCRIPTION

       usage: fasta_formatter [-h] [-i INFILE] [-o OUTFILE] [-w N] [-t] [-e] Part of FASTX Toolkit 0.0.13.2 by gordon@cshl.edu

       [-h]   = This helpful help screen.

       [-i INFILE]
	      = FASTA/Q input file. default is STDIN.

	      [-o OUTFILE] = FASTA/Q output file. default is STDOUT.  [-w N]	   = max. sequence line width for output FASTA file.

	      When  ZERO  (the default), sequence lines will NOT be wrapped - all nucleotides of each sequences will appear on a single line (good
	      for scripting).

       [-t]   = Output tabulated format (instead of FASTA format).

	      Sequence-Identifiers will be on first column, Nucleotides will appear on second column (as single line).

       [-e]   = Output empty sequences (default is to discard them).

	      Empty sequences are ones who have only a sequence identifier, but not actual nucleotides.

   Input Example:
	      >MY-ID AAAAAGGGGG CCCCCTTTTT AGCTN

   Output example with unlimited line width [-w 0]:
	      >MY-ID AAAAAGGGGGCCCCCTTTTTAGCTN

   Output example with max. line width=7 [-w 7]:
	      >MY-ID AAAAAGG GGGTTTT TCCCCCA GCTN

   Output example with tabular output [-t]:
       MY-ID  AAAAAGGGGGCCCCCTTTTAGCTN

       example of empty sequence: (will be discarded unless [-e] is used)

	      >REGULAR-SEQUENCE-1 AAAGGGTTTCCC >EMPTY-SEQUENCE >REGULAR-SEQUENCE-2 AAGTAGTAGTAGTAGT GTATTTTATAT

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.

fasta_formatter 0.0.13.2					     May 2012							FASTA_FORMATTER(1)
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