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The awk regex below produces the current,where
only the matching line are printed. However, I am trying to print all lines in test.txt,
and if the line matches the first regex the word "good" is...

Thank you very much :).

Trying to use awk to calulate a percent based on the count of each matching $5 in file divided by the count of each $7 that is greater than or = to 20. The portion of code before the first | gets the...

Thank you very much :).

I am trying to use bash to loop through a directory /path/to/data using a prefix match from /path/to/file. That match is obtained and works using the code below (in green)... what I can not seem to...

Got it.... if I want to be able to view these var, for say troubleshooting, canI? They can be virtual I just may need to verify them. Thank you :)

I think you beat me to it and just posted.

So if I am understanding the below should write each line in config to script.sh to be able to use as variables? By sourceing . $config the config into memory, that will not print the actual...

if I just print the $line I do see each var printed. However when I re-direct it to the script I do not see them. Are they avaliable to the script to use?

the config file will be different for...

The first parameter starting the script is config, there are two possible choices depending on the data type so I am going to pass it as an argument. Thank you :).


config=$1

set -- $config...

I get: y being echo on a newline. Thankk you :).



mkdir TEST && cd $_
echo -e '. $1\necho var' >script.sh
echo 'var=yes' >config
bash script.sh config
yes



y
y
y


should...

I just want to make sure I am understanding how to pass a config file to a bash script . In the below I pass to arguments to a script, then define them in the script as id and config. I then source...

Thank you all :)

In the below there are two generic .vcf files (genome.S1.vcf and genome.S2.vcf) in a directory. There wont always be two genaric files but I am trying to use bash to rename each of these generic...

I changed the shebang line in the python executable to #!/usr/bin/env python to match the other .py on my system and get the below error.


python --version on centos 7
Python 2.7.5

...

I am running the below loop that to process the 3 bam files (which isn't always the case). A .py executable is then called using | xargs sh to further process. If I just run it with echo the output...

I apologize for the delay in response, the script works perfectly.... thank you very much :).

The id contains the unique prefix of each bam, so the s1,s2,s3,s4.

I am trying to insert each of those into the command in post 3. That is make the command dependent or conditional on id. So if...

I am trying to insert each $id into the standard command below above the ref following the format -- bam ${id} \. There won't always be
4 $id, that will change each time. Maybe storing each $id in...

I currently have a loop that reads all .bam files in a directory (wont always be 4 like in this example,
into $id. What I am trying to do, unsucessfully, is create specific new lines in an exsisting...

Thank you very much :).

The awk below executes and is close (producing the first 4 columns in desired). However, when I add the sum of $7, I get nothing returned. Basically, I am trying to combine all the matching $4 in f1...

Thank you all :).

Using awk to extract value after a keyword in an html, and store in ts. The awk does execute but ts is empty. I use the tag as a delimiter and the keyword as a pattern, but there probably is a better...

Thank you both :).

If any of the below are in $dir then File found was found, moving on.


fileone.csv
fileOne.csv
Fileone.csv
FileOne.csv


If none of those or alike exist, it will echo "File was found and...