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troubleshooting Question

looping in a bash script

Avatar of sebastizz
sebastizz asked on
Mac OS XShell Scripting
6 Comments1 Solution303 ViewsLast Modified:
I have been doing this for hours and I have just given up:...

The task: loop through a folder of files and perform 6 scripts on each file to run as one shell script

Each time a file is processed by one script it gets put in another folder. The intention is to pass the resulting file name to the next script. I dont want to keep the folder path and the original .txt or whatever just the filename and the new file extension. Can anyone help?

The scripts are as follows (on a mac as a shell script)

for each file as $file

$ gzcat $file.fq.gz | ./reformat_sequence_data.rb > ./reformatsequence/$file.txt

$ python qualityMask.py ./reformatsequence/$file.txt  ./qualitymask/$file.seq 20 1

$ ./unique_seq_counts.rb ./qualitymask/$file.seq > ./uniquecounts/$file.counts.txt

$ cut -f1 ./uniquecounts/$file.counts.txt > ./uniqueseq/$file.uniq.seq

$ ./bowtie-1.1.0/bowtie -r -m1 -v1  ./bowtie-1.1.0/indexes/hg19 ./uniqueseq/$file.uniq.seq > ./alignedunique/$file.bowtie.txt
ASKER CERTIFIED SOLUTION
Avatar of omarfarid
Commented:
This problem has been solved!
Unlock 1 Answer and 6 Comments.
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