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Top Forums Shell Programming and Scripting awk to comppare two files using rwo fields Post 302982590 by RavinderSingh13 on Friday 30th of September 2016 12:53:19 PM
Old 09-30-2016
Quote:
Originally Posted by cmccabe
I corrected the input and by compare I mean ls look in file2 for the fields from file1. The awk was an attempt at that. However it seems to only look at one file. Thank you Smilie.
Hello cmccabe,

could you please answer to RudiC's question, along with that I would like to ask you one question too. I see in output as follows.
Code:
hr13   20189510    20189511    GJB2 
chr13   20189546    AC  A   INDEL   ADP=164

In first line first field is hr13 not chr13 so is it a typo? In second line(mentioned above) I didn't see thrid field as 20189546 so in all the time only 3rd field was getting compared and last line 2nd field is getting compared, could you please let us know on these 2 points too.

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
 

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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] [-j file_number field] [-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. (The argument to -a must not be preceded by a space; see the COMPATIBILITY section.) -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 form 'file_number.field', where file_number is a file number and field is a field number. The elements of list must be either comma (``,'') or whitespace separated. (The latter requires quoting 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. 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. (To distinguish between this and -a file_number, join currently requires that the latter not include any white space.) -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_num- ber.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 shell scripts don't require modification and should not be used. SEE ALSO
awk(1), comm(1), paste(1), sort(1), uniq(1) STANDARDS
The join command is expected to be IEEE Std 1003.2 (``POSIX.2'') compatible. BSD
April 28, 1995 BSD
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