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Top Forums Shell Programming and Scripting Use same file selected in first bash process that has matching digits in it fot the second Post 302977923 by pilnet101 on Saturday 23rd of July 2016 02:15:59 PM
Old 07-23-2016
Hi - This is only rough but something like the below should work on your data:

Code:
#!/bin/bash
FILESDIR=/home/cmccabe/Desktop/files
ANNOVARDIR=/home/cmccabe/Desktop/annovar

PS3="please select a file to analyze with a panel: "
select file in ${FILESDIR}/*; do
        [[ -z ${file} ]] && printf "Pick a file" || break
done

filename=${file##*/}
file2=$(ls ${ANNOVARDIR}/${filename%%_*}*)
printf "File 1 is: ${file}\n"
printf "File 2 is: ${file2}\n"

This makes the assumption that:
  • There is only 1 file in the 'annovar' directory which has the same prefix (delimited by an underscore) as the associated file in the 'files' directory and it exists
  • This is not just applicable for '123_' but for all files
This User Gave Thanks to pilnet101 For This Post:
 

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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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