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I have been trying to understand your code and am just not understanding, but I am trying, I know it may seem like I am not but I assure yu that I am and will continue to do so. I added comments to...

ls -l /home/cmccabe/folder/less/*.txt
-rw-rw-r-- 1 cmccabe cmccabe 32254 Dec 7 17:14 /home/cmccabe/folder/less/00-0000_regions.txt
-rw-rw-r-- 1 cmccabe cmccabe 32254 Dec 7 17:14...

I added a couple parameters in the script to pass from the for loop. It does look like the correct files are being passed to the script, however the output is not correct. Commenting out the printf...

I the original code below the bold is the static or the file that is always used. The italics output is set by prefand $file is the underlined portion and would be dependent on each .txt file in the...

There are two .txt files in the directory:


00-0000_regions.txt and 11-1111_regions.txt


these two .txtfiles are $bname and $pref is the digits after the _regions.txt is removed.


for...

I truely appreciate the helpful troubleshooting tips and explanations. I will use them to debug and post back. I did learn as a reseacher and am always trying to refine and improve my technique. I...

If I try to use a for loop on the above script (which I called exon.sh) to define $file I get empty output.


for file in path/to/*.txt ; do
bname=$(basename $file)
...

Thank you very much for your help, I did not realize that there were extra spaces but was able to fix that. Again thank you very much :)

there could potentially be overlap in the $2-$3 value ranges, that is why $4 or the gene id id used because the same $2-$3 values can not exist in two different genes. To be extra sure the...

file2 is a very large file of genes and all associated coding exons. So, using the SDHB gene, as an example, that is one of the ~22,000 genes in the human genome. A gene is made up a variable exons,...

The $4 value in file1 is not unique but is meant to ensure that, using line 1 as an example, only SDBH lines are searched or used in the comparison. There may be hundreds of lines in file1, but only...

I am trying to use awk to check if each $2 in file1 falls between $2 and $3 of the matching $4 line of file2. If it does then in $5 of file2, exon if it does not intron. I think the awk below will do...