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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) 						    BSD General Commands Manual 						   JOIN(1)

NAME
join -- relational database operator SYNOPSIS
join [-a file_number | -v file_number] [-e string] [-o list] [-t char] [-1 field] [-2 field] file1 file2 DESCRIPTION
The join utility performs an ``equality join'' on the specified files and writes the result to the standard output. The ``join field'' is the field in each file by which the files are compared. The first field in each line is used by default. There is one line in the output for each pair of lines in file1 and file2 which have identical join fields. Each output line consists of the join field, the remaining fields from file1 and then the remaining fields from file2. The default field separators are tab and space characters. In this case, multiple tabs and spaces count as a single field separator, and leading tabs and spaces are ignored. The default output field separator is a single space character. Many of the options use file and field numbers. Both file numbers and field numbers are 1 based, i.e. the first file on the command line is file number 1 and the first field is field number 1. The following options are available: -a file_number In addition to the default output, produce a line for each unpairable line in file file_number. -e string Replace empty output fields with string. -o list The -o option specifies the fields that will be output from each file for each line with matching join fields. Each element of list has the either the form 'file_number.field', where file_number is a file number and field is a field number, or the form '0' (zero), representing the join field. The elements of list must be either comma (``,'') or whitespace separated. (The latter requires quot- ing to protect it from the shell, or, a simpler approach is to use multiple -o options.) -t char Use character char as a field delimiter for both input and output. Every occurrence of char in a line is significant. -v file_number Do not display the default output, but display a line for each unpairable line in file file_number. The options -v 1 and -v 2 may be specified at the same time. -1 field Join on the field'th field of file 1. -2 field Join on the field'th field of file 2. When the default field delimiter characters are used, the files to be joined should be ordered in the collating sequence of sort(1), using the -b option, on the fields on which they are to be joined, otherwise join may not report all field matches. When the field delimiter char- acters are specified by the -t option, the collating sequence should be the same as sort(1) without the -b option. If one of the arguments file1 or file2 is ``-'', the standard input is used. DIAGNOSTICS
The join utility exits 0 on success, and >0 if an error occurs. COMPATIBILITY
For compatibility with historic versions of join, the following options are available: -a In addition to the default output, produce a line for each unpairable line in both file 1 and file 2. -j1 field Join on the field'th field of file 1. -j2 field Join on the field'th field of file 2. -j field Join on the field'th field of both file 1 and file 2. -o list ... Historical implementations of join permitted multiple arguments to the -o option. These arguments were of the form 'file_number.field_number' as described for the current -o option. This has obvious difficulties in the presence of files named '1.2'. These options are available only so historic shellscripts don't require modification and should not be used. STANDARDS
The join command conforms to IEEE Std 1003.1-2001 (``POSIX.1''). SEE ALSO
awk(1), comm(1), paste(1), sort(1), uniq(1) BSD
April 18, 2002 BSD
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