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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) 							   User Commands							   comm(1)

NAME
comm - select or reject lines common to two files SYNOPSIS
comm [-123] file1 file2 DESCRIPTION
The comm utility reads file1 and file2, which must be ordered in the current collating sequence, and produces three text columns as output: lines only in file1; lines only in file2; and lines in both files. If the input files were ordered according to the collating sequence of the current locale, the lines written will be in the collating sequence of the original lines. If not, the results are unspecified. OPTIONS
The following options are supported: -1 Suppresses the output column of lines unique to file1. -2 Suppresses the output column of lines unique to file2. -3 Suppresses the output column of lines duplicated in file1 and file2. OPERANDS
The following operands are supported: file1 A path name of the first file to be compared. If file1 is -, the standard input is used. file2 A path name of the second file to be compared. If file2 is -, the standard input is used. USAGE
See largefile(5) for the description of the behavior of comm when encountering files greater than or equal to 2 Gbyte ( 2^31 bytes). EXAMPLES
Example 1 Printing a list of utilities specified by files If file1, file2, and file3 each contain a sorted list of utilities, the command example% comm -23 file1 file2 | comm -23 - file3 prints a list of utilities in file1 not specified by either of the other files. The entry: example% comm -12 file1 file2 | comm -12 - file3 prints a list of utilities specified by all three files. And the entry: example% comm -12 file2 file3 | comm -23 -file1 prints a list of utilities specified by both file2 and file3, but not specified in file1. ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of comm: LANG, LC_ALL, LC_COLLATE, LC_CTYPE, LC_MESSAGES, and NLSPATH. EXIT STATUS
The following exit values are returned: 0 All input files were successfully output as specified. >0 An error occurred. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWesu | +-----------------------------+-----------------------------+ |CSI |enabled | +-----------------------------+-----------------------------+ |Interface Stability |Standard | +-----------------------------+-----------------------------+ SEE ALSO
cmp(1), diff(1), sort(1), uniq(1), attributes(5), environ(5), largefile(5), standards(5) SunOS 5.11 3 Mar 2004 comm(1)
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