each input file is a tsv of 40 columns, the below is an example of multiple lines (I only show 4 columns, as all 40 are the same or close to it and the script does produce the desired output). The problem I am having is that if there and Additional CNV detected as in output 1, then the script works printing Additional CNV detected followed by the line or lines.
If there are No Additional CNV detected as in output 2, that line prints multiple times (presumably 2800 because that is the total lines).
I am using ubuntu 14.04 as my OS.
Post 1 is actual output produces with the complete files, but to keep the post easier to read I only used several lines.
The output is close as is, I just cant seem to solve why No Additional CNV detected repeats. Thank you very much .
file
Code:
chr1:11184539 CNV 5%:5.5,95%:2.68 Name
chr1:11184539 REF
chr1:11184539 SNV A
chr1:11184555 CNV 5%:0.9,95%:1.9 BRCA1
chr1:11184539 FUSION
chr1:11184539 INDEL G
chr1:11184555 CNV 5%:2.5,95%:2.68 Name2
chr1:11184555 CNV 5%:1.1,95%:1.8 BRCA2
Yes, the code you have shown us is easy to understand. And, with or without sample input files, we can easily say that most of the output you have shown did not come from the code you have shown us.
We have no reason not to believe that the code you have not shown us is what is producing the extra output that you don't want.
I asked what files were being processed. You didn't answer. For all we know, there are hundreds of files being processed by your loop with many of them adding a line to the output you say you don't want.
I asked for sample input files and you showed us a sample with at most 4 input fields that is being fed into code you showed us that is evaluating data found in fields 12 and 14.
You have made it very clear that you want us to explain why code you won't show us won't work with data you won't show us using filenames you won't show us. I wish you luck, but I can't help you under these conditions.
This User Gave Thanks to Don Cragun For This Post:
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