Full Discussion: finding max size
Top Forums Shell Programming and Scripting finding max size Post 302555433 by Corona688 on Wednesday 14th of September 2011 05:48:38 PM
That's what I get for answering too fast... Here's a solution that does what you want:

$ awk '{       A[ $1 "#" $2 ]++;       }
END {   for(K in A)
                split(K, L, "#");
                STR=L[1]        ;       VAL=L[2]

                if(C[STR] <= A[K])

        for(K in T)     print K, T[K];
} < data

There's an inconsistency in your example though. If we get a pattern like
A 1
A 1
A 2
A 2

which should be chosen, 1 or 2? Your example has ABC choosing the first max and DEF choosing the last max...

To choose the first instead of the last, change
if(C[STR] <= A[K])

if(C[STR] < A[K])

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RE-PCR(1)						      General Commands Manual							 RE-PCR(1)

re-PCR -- Find sequence tagged sites (STS) in DNA sequences SYNOPSIS
re-PCR [-hV] -p hash-file [-g gaps] [-n mism] [-lq] [primer ...] re-PCR [-hV] -P hash-file [-g gaps] [-n mism] [-l] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [primers-file ...] re-PCR [-hV] -s hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-o outfile] [-r+|-] [left right lo[-hi] [...]] re-PCR [-hV] -S hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [stsfile ...] DESCRIPTION
Implements reverse searching (called Reverse e-PCR) to make it feasible to search the human genome sequence and other large genomes by per- forming STS and primer searches. OPTIONS
-p=hash-file Perform primer lookup using hash-file -P=hash-file Perform primer lookup using hash-file -s=hash-file Perform STS lookup using hash-file -S=hash-file Perform STS lookup using hash-file -n=mism Set max allowed mismatches per primer for lookup -g=gaps Set max allowed indels per primer for lookup -m=margin Set variability for STS size for lookup -l Use presize alignments (only if gaps>0) -G Print alignments in comments -d=min-max Set default STS size -r=+|- Enable/disable reverse STS lookup -O=+|- Enable/disable syscall optimisation -C=batchcnt Set number of STSes per batch -o=outfile Set output file name -q Quiet (no progress indicator) EXAMPLE
famap -tN -b genome.famap org/chr_*.fa fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200 See famap(1) and fahash(1) SEE ALSO
/usr/share/doc/ncbi-epcr/README.txt bioperl(1), e-pcr(1), famap(1) and fahash(1) AUTHORS
This manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. April 2008 RE-PCR(1)

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