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Create Files From Double For Cycle

Dear all, I create a code like this, which solve my problem to separate bam file to each segments, but still time I have one problem and I cannot finish it. I would like to create many outputs (files), which has name, same like variable $h. Than I want one think, if the for cycle for "h" finished, the code create a text fie with same name like $h.txt . I tried this, but it doesnt work:

 #!/bin/bash 
 for h in {1..22..1} 
 do 
 for i in {0..249480000..60000}
 do 
 u=$i let "u +=60000"

 echo $i"-"$u | samtools view /home/filip/Desktop/Posledni\ NIFTY/019/odfiltrovany019.bam  chr$h:$i-$u | awk '{ n=length($10);print gsub(/[GCCgcs]/,"",$10)/n;}'| awk '{s+=$1}END{print NR,s/NR}' > ${h%}.txt

 done  
 done

OTUPUT will be 1.txt, 2.txt, 3.txt, ......., 22.txt. This file will contain information from loop cycle for variable i. Thank you.

output bash awk
• 3,358 views • link
updated by Giovanni M Dall'Olio Giovanni M Dall'Olio • written by filipzembol filipzembol

maybe I am slow this morning but I do not fully understand the question plus the title is somewhat misleading. Could you put an example of the type of output you want ?

• 18 views • link
written by Gabriel R. Gabriel R.

I do not know, how could I use > ${h%}.txt , because I want to receive on output txt files, which have name same like variable h. The code i OK, but I do not know how use the output syntax, after each loop (for variable h) I recieve one file with same name (1..22) and it will be filled by loop (for i).

• 0 views • link
written by filipzembol filipzembol

This question is hardly bioinformatics related, apart from the samtools command. Also, I still don't understand what you're asking.

• 0 views • link
updated by Ram Ram • written by David Westergaard David Westergaard

1 answer

I would do it using GNU/parallel. See Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them.

Basically, once you have installed GNU/parallel (not the parallel tool that comes with some linux distributions), you can convert your loop to something like the following:

$: parallel 'chromosome={1}; start={2}; end=$(echo "$start"+60000|bc); echo $chromosome $start $end' ::: $(seq 1 22) ::: $(seq 0 60000 249480000)
1 0 60000
1 60000 120000
1 120000 180000
1 180000 240000
1 240000 300000
1 300000 360000
1 360000 420000
1 420000 480000
1 480000 540000
1 540000 600000
1 600000 660000
1 660000 720000
1 720000 780000
1 780000 840000
 .........

Now, you can modify your original command, substituting $h, $i and $u with $chromosome, $start, and $end (if I interpreted your code correctly)

• 12 views • link
written by Giovanni M Dall'Olio Giovanni M Dall'Olio

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