Using while loop to go over all files in a folder
Hi,
I am currently running fastx_trimmer tool in order to trim all my paired end RNAseq input files using while loop.
The filenames are as follows:
1_1.fastq
1_2.fastq
2_1.fastq
2_2.fastq
.................
25_1.fastq
25_2.fastq
Below is the code that I use to run the while loop in a bash script using byobu screen
#!/usr/bin
i=1
while [ $i -le 25 ]
do
cd fastq
cd unzip_fastq
fastx_trimmer -Q33 -f 1 -l 100 -i $i_1.fastq -o $i_1_trimmed.fastq
mv $i_1_trimmed.fastq ../trimmed_fastq
fastx_trimmer -Q33 -f 1 -l 100 -i $i_2.fastq -o $i_2_trimmed.fastq
mv $i_2_trimmed.fastq ../trimmed_fastq
cd ~
((i++))
done
But, I got the follow error.
fastx_trimmer: failed to open input file '.fastq': No such file or directory
Any help is much appreciated. Thanks in advance
Catherine
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Ram
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3 answers
You can try the following, which is slightly simpler and you can move your files after with mv
for i in folderWithFastqFiles/*.fastq
do
fastx_trimmer -Q33 -f 1 -l 100 -i $i -o $i.trimmed.fastq
done
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Ram
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Eric Normandeau
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Eric Normandeau
True. It's an old habit :) I edited my script to simplify it.
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Eric Normandeau
maybe try this one:
mkdir $2 #delete this if output directory already exists...
for f in $1/*
do
if [ -f $f ]
then
fastx_trimmer -Q33 -f 1 -l 100 -i $f -o $2/$(basename $f .fastq)_trimmed.fastq
fi
done
Call it with first argument as path to your fastq and second argumant as path where to store the trimmed files.
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Seems that files are not in correct directories else code seems correct!!
_is a valid character in a variable name. So it thinks you are looking for a variable names$i_1_trimmed.fastq. You should instead use${i}_1_trimmed.fastq.In addition, you can get more informative messages about errors if you put
set -exat the top of your script.or you could escape it with:
$i\_1_trimmed.fastq...Thank you very much!! By using
${i}, it's working!!!