Hi!
I wrote the following little bash script:
and I get the error:
"Unexpected token near done" at the last two lines.
Unfortunately, I dont know why...
I already checked cat -v file.sh, but there do not seem to be unexpected characters or something...
Do you have any idea?
Greetings!
I wrote the following little bash script:
Code:
echo Processing... inputDir="/home/j490h/localhome/fastq/" output_folder="/home/j490h/localhome/fastq/textfiles/" for input_FASTQfile in `ls ${inputDir}/*fastq*` do filename_only=`basename ${input_FASTQfile}` echo ${filename_only} zcat ${filename_only} | sed -n '1~4p' > ${output_folder}/${filename_only}_ReadIDs.txt done output_folder2="/home/j490h/localhome/fastq/textfiles/combined_textfiles/" trimmed="trimmed" shuffled="shuffled" reconstructed="reconstructed" for file1 in `ls ${output_folder}/*txt*` do for file2 in `ls ${output_folder}/*txt*` do if [ ${trimmed} in ${file1} & ${file2} ] then cat ${file1} ${file2} > ${output_folder2}/${file1}_${file2}_combined.txt elif [ ${shuffled} in ${file1} & ${file2} ] then cat ${file1} ${file2} > ${output_folder2}/${file1}_${file2}_combined.txt elif [ ${reconstructed} in ${file1} & ${file2} ] then cat ${file1} ${file2} > ${output_folder2}/${file1}_${file2}_combined.txt else echo Invalid input FASTQfile done done
"Unexpected token near done" at the last two lines.
Unfortunately, I dont know why...
I already checked cat -v file.sh, but there do not seem to be unexpected characters or something...
Do you have any idea?
Greetings!
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