bash loop to python loop for google colabs

bash loop to python loop for google colabs

1

Hi there,

I have a bash loop to use kallisto on my sequencing samples, but I’m trying now to run kb on google colabs (all the fastq files are on Google drive), so I’d appreciate a hand in ‘translating it to python’.
Here’s the original script:

#
#/bin/bash
FASTQ="/content/drive/My Drive/NovaSeq_raw_data/"
##############
cd $FASTQ
for FILE in $(ls *.fastq.gz | rev| cut -c 24- |rev| cut -c 14- |uniq)
do
echo "kallisto for" $FILE
kallisto quant -i $index.idx -o $FILE -b 100 "${FASTQ}WTCHG_702270_${FILE}_1.fastq.gz" "${FASTQ}WTCHG_702270_${FILE}_2.fastq.gz" "${FASTQ}WTCHG_705748_${FILE}_1.fastq.gz" "${FASTQ}WTCHG_705748_${FILE}_2.fastq.gz"
done


python


loop


kallisto


colabs

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