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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 302977927 by pilnet101 on Saturday 23rd of July 2016 03:24:37 PM
Old 07-23-2016
Sorry about that, I've amended the script slightly so it should work as expected now:

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 $(cd ${FILESDIR};ls *); do
        [[ -z ${file} ]] && printf "Pick a file" || break
done

file1=${FILESDIR}/${file}
file2=$(ls ${ANNOVARDIR}/${file%%_*}*)
printf "File 1 is: ${file1}\n"
printf "File 2 is: ${file2}\n"

It looks like basename isn't really required as you are dealing with the file names themselves straight from the select loop. Then when you create the file1 variable you append the directory in front of it.
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h5diff(1)						      General Commands Manual							 h5diff(1)

NAME
h5diff - Compares two HDF5 files and reports the differences. SYNOPSIS
h5diff file1 file2 [OPTIONS] [object1 [object2 ] ] DESCRIPTION
h5diff is a command line tool that compares two HDF5 files, file1 and file2, and reports the differences between them. Optionally, h5diff will compare two objects within these files. If only one object, object1, is specified, h5diff will compare object1 in file1 with object1 in file2. In two objects, object1 and object2, are specified, h5diff will compare object1 in file1 with object2 in file2. These objects must be HDF5 datasets. object1 and object2 must be expressed as absolute paths from the respective file's root group. Additional information, with several sample cases, can be found in the document H5diff Examples. OPTIONS
file1 file2 The HDF5 files to be compared. -h Print all differences. -r Print only the names of objects that differ; do not print the differences. These objects may be HDF5 datasets, groups, or named datatypes. -n count Print difference up to count differences, then stop. count must be a positive integer. -d delta Print only differences that are greater than the limit delta. delta must be a positive number. The comparison criterion is whether the absolute value of the difference of two corresponding values is greater than delta (e.g., |a-b| > delta, where a is a value in file1 and b is a value in file2). -p relative Print only differences that are greater than a relative error. relative must be a positive number. The comparison criterion is whether the absolute value of the difference 1 and the ratio of two corresponding values is greater than relative (e.g., |1-(b/a)| > relative where a is a value in file1 and b is a value in file2). object1 object2 Specific object(s) within the files to be compared. EXAMPLES
The following h5diff call compares the object /a/b in file1 with the object /a/c in file2: h5diff file1 file2 /a/b /a/c This h5diff call compares the object /a/b in file1 with the same object in file2: h5diff file1 file2 /a/b And this h5diff call compares all objects in both files: h5diff file1 file2 SEE ALSO
h5dump(1), h5ls(1), h5repart(1), h5import(1), gif2h5(1), h52gif(1), h5perf(1) h5diff(1)
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