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Full Discussion: Deleting sequences based on character frequency
Top Forums Shell Programming and Scripting Deleting sequences based on character frequency Post 302430446 by Scrutinizer on Thursday 17th of June 2010 03:33:58 PM
Old 06-17-2010
Hi, I think I understand what you mean, for the first question:
Code:
awk '{ for (i=1;i<=length($5);i++) F[(substr($5,i,1)),i]+=$4; A[NR]=$0; S[NR]=$5}
     END {for (j=1;j<=NR;j++){{p=1; for(i=1;i<=length(S[j]);i++) if(F[(substr(S[j],i,1)),i]<=5) p=0} if (p){print A[j]}}}' RS=">" ORS=">" infile

If your file is really big and you run out of memory then you could try this
Code:
awk 'NR==FNR { for (i=1;i<=length($5);i++) F[(substr($5,i,1)),i]+=$4; next }
     {p=1; for(i=1;i<=length($5);i++) if(F[(substr($5,i,1)),i]<=5) p=0} p' RS=">" ORS=">" infile infile

Output first Sample:
Code:
> ID 2 Prev 31
A-TGCTAGCTACGTCGTACGT
> ID 3 Prev 30
A-TGCTAGCTACGTCGTTCGT
> ID 4 Prev 30
A-TGCTAGCTACGTCGTACGA

Output second sample:
Code:
> Seq 1 Freq 1
ATC
> Seq 2 Freq 33
ACG
> Seq 3 Freq 33
TTG
> Seq 4 Freq 33
TCC

 

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LEARN ABOUT MOJAVE

tcl_backslash

Tcl_Backslash(3)					      Tcl Library Procedures						  Tcl_Backslash(3)

__________________________________________________________________________________________________________________________________________________

NAME

       Tcl_Backslash - parse a backslash sequence

SYNOPSIS

       #include <tcl.h>

       char
       Tcl_Backslash(src, countPtr)

ARGUMENTS

       char *src (in)		    Pointer to a string starting with a backslash.

       int *countPtr (out)	    If countPtr is not NULL, *countPtr gets filled in with number of characters in the backslash sequence, includ-
				    ing the backslash character.
_________________________________________________________________

DESCRIPTION

       The use of Tcl_Backslash is deprecated in favor of Tcl_UtfBackslash.

       This is a utility procedure provided for backwards compatibility with non-internationalized Tcl extensions.  It parses a backslash sequence
       and returns the low byte of the Unicode character corresponding to the sequence.  Tcl_Backslash modifies *countPtr to contain the number of
       characters in the backslash sequence.

       See the Tcl manual entry for information on the valid backslash sequences.  All of the sequences described in the Tcl manual entry are sup-
       ported by Tcl_Backslash.

SEE ALSO

       Tcl(n), Tcl_UtfBackslash(3)

KEYWORDS

       backslash, parse

Tcl									8.1							  Tcl_Backslash(3)
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