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Bash loop one liner

I am performing a bash loop one liner:.

for k in */centrifuge/kreport/*.txt; do cat $k | cut -f 1,3 > /krona/$k.krona; echo $k; done

The file hierarchy is as follows:

\Drain_4 
    \centrifuge
        \kreport
           A6_kreport.txt
           A4_kreport.txt
           A5_kreport.txt
           \krona
\Drain_5
\Drain_7

Where \ denotes a directory. This is the error i am getting:

-bash: /krona/Drains_2/centrifuge/kreport/A4_kreport.txt: No such file or directory

I am trying to output the file into the krona directory which is in the working directory however when i try to i get that error. When i remove the "/krona" after > the code execute fine so guessing i am having problems with telling it where to output the file but i can't work it out. Any help would be greatly appreciated.

liner loop centrifuge bash
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updated by iraun iraun • written by matt81rd • matt81rd

Do you actually need /krona/ (in the root folder) or rather just krona/ in the current directory?

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written by WouterDeCoster WouterDeCoster

Ideally i would like a folder in the same directory as the three kreport.txt files which contains the results (the altered version of these three files). Drain_5 and Drain_7 also have the same file structure so hopefully the loop will produce the same result as well.

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written by matt81rd • matt81rd

1 answer

$k variable contains the full path to the input file you are parsing. Doing something like this (not tested) should fix the problem:

name=$(basename $k)

And then

> /krona/$name.krona

Try this:

for k in */centrifuge/kreport/*.txt; do
 name=$(basename $k);
 cat $k | cut -f 1,3 > /krona/$name.krona;
 echo $k;
 done
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written by iraun iraun

Hey thanks for your comment!

(note i realised i was working on the wrong results folder now in "results" instead of "kreport" which is why there is a change to the file and folder names but the problem is still the same)

I tried out your suggestion:

for k in */centrifuge/results/*.txt; do name=$(basename $k); cat $k | cut -f 1,3 > /krona/$name.krona; echo $k; done

but am still getting the following error:

    -bash: /krona/A4_results.txt.krona: No such file or directory
Drains_2/centrifuge/results/A4_results.txt
-bash: /krona/B1_results.txt.krona: No such file or directory
Drains_2/centrifuge/results/B1_results.txt
-bash: /krona/B6_results.txt.krona: No such file or directory
Drains_2/centrifuge/results/B6_results.txt
-bash: /krona/D1_results.txt.krona: No such file or directory
Drains_2/centrifuge/results/D1_results.txt
-bash: /krona/E4_results.txt.krona: No such file or directory
Drains_2/centrifuge/results/E4_results.txt
-bash: /krona/NC_D2_results.txt.krona: No such file or directory
Drains_2/centrifuge/results/NC_D2_results.txt
-bash: /krona/C4_results.txt.krona: No such file or directory
Drains_4/centrifuge/results/C4_results.txt
-bash: /krona/D3_results.txt.krona: No such file or directory
Drains_4/centrifuge/results/D3_results.txt
-bash: /krona/E7_results.txt.krona: No such file or directory
Drains_4/centrifuge/results/E7_results.txt
-bash: /krona/G1_results.txt.krona: No such file or directory
Drains_4/centrifuge/results/G1_results.txt
-bash: /krona/I1_results.txt.krona: No such file or directory
Drains_4/centrifuge/results/I1_results.txt
-bash: /krona/I8_results.txt.krona: No such file or directory
Drains_4/centrifuge/results/I8_results.txt
-bash: /krona/NC_D4_results.txt.krona: No such file or directory
Drains_4/centrifuge/results/NC_D4_results.txt
-bash: /krona/A7_results.txt.krona: No such file or directory
Drains_6/centrifuge/results/A7_results.txt
-bash: /krona/B4_results.txt.krona: No such file or directory
Drains_6/centrifuge/results/B4_results.txt
-bash: /krona/B7_results.txt.krona: No such file or directory
Drains_6/centrifuge/results/B7_results.txt
-bash: /krona/C10_results.txt.krona: No such file or directory
Drains_6/centrifuge/results/C10_results.txt
-bash: /krona/C1_results.txt.krona: No such file or directory
Drains_6/centrifuge/results/C1_results.txt
-bash: /krona/D7_results.txt.krona: No such file or directory
Drains_6/centrifuge/results/D7_results.txt
-bash: /krona/NC_D6_results.txt.krona: No such file or directory
Drains_6/centrifuge/results/NC_D6_results.txt
-bash: /krona/A6_results.txt.krona: No such file or directory
Drains_7/centrifuge/results/A6_results.txt
-bash: /krona/A8_results.txt.krona: No such file or directory
Drains_7/centrifuge/results/A8_results.txt
-bash: /krona/C7_results.txt.krona: No such file or directory
Drains_7/centrifuge/results/C7_results.txt
-bash: /krona/C9_results.txt.krona: No such file or directory
Drains_7/centrifuge/results/C9_results.txt
-bash: /krona/G6_results.txt.krona: No such file or directory
Drains_7/centrifuge/results/G6_results.txt
-bash: /krona/H1_results.txt.krona: No such file or directory
Drains_7/centrifuge/results/H1_results.txt
-bash: /krona/NC_D7_results.txt.krona: No such file or directory
Drains_7/centrifuge/results/NC_D7_results.txt

It is looping and showing me that at least its finding the files i want it to execute on but its still giving me the same error. Sorry for not being very useful in giving you more information to help.

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written by matt81rd • matt81rd

Where do you want to save the results? If you want to save them in your current working directory, you could simply do this:

for k in */centrifuge/kreport/*.txt; do
 name=$(basename $k);
 cat $k | cut -f 1,3 > $name.krona;
 echo $k;
 done

If you want the result files in any other specific folder, then you could do something like this:

for k in */centrifuge/kreport/*.txt; do
 outputdir="/insert/here/your/path"; #Make sure that the path exists 
 name=$(basename $k);
 cat $k | cut -f 1,3 > $outputdir/$name.krona;
 echo $k;
 done

I hope this helps.

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written by iraun iraun

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