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Top Forums Shell Programming and Scripting Finding most common substrings Post 302890005 by verse123 on Monday 24th of February 2014 05:30:11 PM
Old 02-24-2014
thanks, don. I have 2 last questions.

Some helpful individuals from the forums helped with this code below but it seems to be generating the same output for any string pattern I give it when I run it with a large file (200GB). However, when I run it with a small test file, that output is different for each string. Why do you think this could be happening?

Also, am I recording the length appropriately for all of the column 2 lines that have the same ID from column 1? Here's the code:


Code:
JOIN="joined.join"
cod1="ypehe"
cod2="edog"

awk '
        NR==1{
                print "ID", "cod_freq", "ID_freq", "length"
                next
             }
      FNR==NR{
                A[$1]++
                B[$1]+=gsub(/'${cod1}' || '${cod2}'/,x, $2)
                C[$1]+=length($2)
                next
             } 
    ($1 in A){ 
                print $1,B[$1],A[$1],C[$1]
                delete A[$1]
                delete B[$1]
                delete C[$1]
             }

    ' OFS='\t' ${JOIN}.out{,} > ${JOIN}.freq

 

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JOIN(1) 							   User Commands							   JOIN(1)

NAME
join - join lines of two files on a common field SYNOPSIS
join [OPTION]... FILE1 FILE2 DESCRIPTION
For each pair of input lines with identical join fields, write a line to standard output. The default join field is the first, delimited by blanks. When FILE1 or FILE2 (not both) is -, read standard input. -a FILENUM also print unpairable lines from file FILENUM, where FILENUM is 1 or 2, corresponding to FILE1 or FILE2 -e EMPTY replace missing input fields with EMPTY -i, --ignore-case ignore differences in case when comparing fields -j FIELD equivalent to '-1 FIELD -2 FIELD' -o FORMAT obey FORMAT while constructing output line -t CHAR use CHAR as input and output field separator -v FILENUM like -a FILENUM, but suppress joined output lines -1 FIELD join on this FIELD of file 1 -2 FIELD join on this FIELD of file 2 --check-order check that the input is correctly sorted, even if all input lines are pairable --nocheck-order do not check that the input is correctly sorted --header treat the first line in each file as field headers, print them without trying to pair them -z, --zero-terminated line delimiter is NUL, not newline --help display this help and exit --version output version information and exit Unless -t CHAR is given, leading blanks separate fields and are ignored, else fields are separated by CHAR. Any FIELD is a field number counted from 1. FORMAT is one or more comma or blank separated specifications, each being 'FILENUM.FIELD' or '0'. Default FORMAT outputs the join field, the remaining fields from FILE1, the remaining fields from FILE2, all separated by CHAR. If FORMAT is the keyword 'auto', then the first line of each file determines the number of fields output for each line. Important: FILE1 and FILE2 must be sorted on the join fields. E.g., use "sort -k 1b,1" if 'join' has no options, or use "join -t ''" if 'sort' has no options. Note, comparisons honor the rules specified by 'LC_COLLATE'. If the input is not sorted and some lines cannot be joined, a warning message will be given. AUTHOR
Written by Mike Haertel. REPORTING BUGS
GNU coreutils online help: <http://www.gnu.org/software/coreutils/> Report join translation bugs to <http://translationproject.org/team/> COPYRIGHT
Copyright (C) 2017 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. SEE ALSO
comm(1), uniq(1) Full documentation at: <http://www.gnu.org/software/coreutils/join> or available locally via: info '(coreutils) join invocation' GNU coreutils 8.28 January 2018 JOIN(1)
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