Working with the Unix Shell 2

Exercise 1.1. Download a compressed data archive from https://www.dropbox.com/s/vivut71p4bkurhw/data.tar.gz (10 points)

Exercise 1.2. Regenerate the original data folder from data.tar.gz. Change directory into the data folder. List the files in the folder. (10 points)

Exercise 1.3. Check if any files have been corrupted using the MDFSUM checksum file and note its FILENAME. Delete any corrupted files. (10 points)

Exercise 1.4. Replace the corrupted file with a correct copy from https://www.dropbox.com/s/vf8qcoj07mcq7wn/FILENAME. You will need to replace FILENAME with the correct filename as noted earlier. Check that there are no more md5sum errors. Go back to the original directory. (10 points)

Exercise 2.1. (20 points) Write a script extract.sh that extracts only the raw sequence letters and quality scores from a FASTQ file. For example, if test.fq consists of

@071112_SLXA-EAS1_s_7:5:1:817:345
GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC
+071112_SLXA-EAS1_s_7:5:1:817:345
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9IC
@071112_SLXA-EAS1_s_7:5:1:801:338
GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGA
+071112_SLXA-EAS1_s_7:5:1:801:338
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBI

then

cat test.fq | extract.sh

should print

GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9IC
GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGA
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBI

For all of Exercise 2, create test.fq, and run your script on test.fq to check that it gets the expected results.

Exercise 2.2 (20 points) Write a script extract_seq.sh that extracts only the raw sequence letters from a FASTQ file and combines them into a single string. For example,

cat test.fq | bash extract_seq.sh

should print

GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCGTTCAGGGATACGACGTTTGTATTTTAAGAATCTGA

Exercise 2.3 Write a script calc_gc.sh that estimates the GC ratio (the fraction of all bases that are either G or C) from a FASTQ file. For example, the GC ratio of test.fq is .5138, (20 points)