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Perl command in bash

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# 1  
Old 03-27-2015
Perl command in bash
I have the below perl script that runs (I think):

Code:
 'C:\Users\cmccabe\Desktop\annovar\matrix.pl' < "${id}".txt.hg19_multianno.txt > "L:\NGS\3_BUSINESS\Matrix\Torrent\matrix_${id}.txt"

The problem is I get an error that the ${id}.txt does not exist. I have tried "${id}.txt as well. There is a file (attached) with the id in it as well but can sed or awk be used to extract this id from the file and put it in the perl command?

For example, snp.txt is the first line of target.txt - can that value be extracted and substituted for the ${id).txt in the perl . Also, if there are multiple lines can it loop through one at a time? Thank you Smilie.
# 2  
Old 03-27-2015
I suspect that, when it says file not found, it means what it says, file not found.

Check for things like typos in the filename, unwanted spaces or carriage returns in the id variable, etc.
# 3  
Old 03-27-2015
it seems that you run perl in windows, not in unix or linux. what is the posix environment you use? which shell?
# 4  
Old 03-27-2015
I suspect it might be Cygwin, but let's hear it from the OP.
# 5  
Old 03-28-2015
Yes, the posix environment is cygwin and I am using
Code:
 bash

to run the perl script. Thank you Smilie.
# 6  
Old 03-28-2015
And what is the value of $id?
# 7  
Old 03-28-2015
Why don't you concatenate all your threads (e.g. this) about that one topic into one?
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