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Top Forums Shell Programming and Scripting combine lines from two files based on an if statement Post 302561248 by Cheri on Monday 3rd of October 2011 04:43:37 PM
Old 10-03-2011
combine lines from two files based on an if statement

I'm rather new to programming, and am attempting to combine lines from 2 files in a way that is way beyond my expertise - any help would be appreciated!

I need to take a file (file1) and add columns to it from another file (file2). However, a line from file2 should only be added to a given line in file1 if the number in file1column2 is between the numbers in file2column4 and file2column5. Therefore, I don't think I can use paste or join, and I can't figure out how to combine awk with getline or some if statement to get this to work. Any insight would be appreciated! Thanks so much!

file1
Code:
chr2L    22975381    -1.6723247    chr2L    22975381    -1.8917731    0.219448    0
chr2L    22975421    -1.526086    chr2L    22975421    -1.8669024    0.340816    0    
chr2L    22975458    -1.7168827    chr2L    22975458    -1.9361134    0.219231    0

file2
Code:
2L    gadfly    exon    15748693    15748925    .    -    
2L    gadfly    exon    15748515    15748637    .    -    
2L    gadfly    exon    15746596    15748455    .    -

Moderator's Comments:
Mod Comment
Please use code tags when posting data and code samples!

Last edited by vgersh99; 10-03-2011 at 06:04 PM.. Reason: code tags, please!
 

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COMM(1) 						    BSD General Commands Manual 						   COMM(1)

NAME
comm -- select or reject lines common to two files SYNOPSIS
comm [-123i] file1 file2 DESCRIPTION
The comm utility reads file1 and file2, which should be sorted lexically, and produces three text columns as output: lines only in file1; lines only in file2; and lines in both files. The filename ``-'' means the standard input. The following options are available: -1 Suppress printing of column 1. -2 Suppress printing of column 2. -3 Suppress printing of column 3. -i Case insensitive comparison of lines. Each column will have a number of tab characters prepended to it equal to the number of lower numbered columns that are being printed. For example, if column number two is being suppressed, lines printed in column number one will not have any tabs preceding them, and lines printed in column number three will have one. The comm utility assumes that the files are lexically sorted; all characters participate in line comparisons. ENVIRONMENT
The LANG, LC_ALL, LC_COLLATE, and LC_CTYPE environment variables affect the execution of comm as described in environ(7). EXIT STATUS
The comm utility exits 0 on success, and >0 if an error occurs. SEE ALSO
cmp(1), diff(1), sort(1), uniq(1) STANDARDS
The comm utility conforms to IEEE Std 1003.2-1992 (``POSIX.2''). The -i option is an extension to the POSIX standard. HISTORY
A comm command appeared in Version 4 AT&T UNIX. BUGS
Input lines are limited to LINE_MAX (2048) characters in length. BSD
January 26, 2005 BSD
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