Linux

This repository will be containing exercises and my journey with learning Bash and linux terminal

questions and solutions

1. Create a project directory called Exercise. Which commands did you use?

mkdir exercise

2. In the directory, create all the sub-directories you would need for a Bioinformatics Project

mkdir -p data scripts results
cd data
mkdir -p Raw Processed

3. With the provided dataset files, put them in the appropriate directories you created under your Bioinformatics Project

cp exercise .
cp *.fa ./Raw

4. Extract the sequence headers and save into a file sequence_names.txt in the appropriate directory

cat *.fa >> joined.fa
grep "^>" joined.fa > sequence_names.txt 
mv sequence_name.txt ../Processed

5. Save the commands you used in question 4 in a script file extract_seq.sh

vim extract_seq.sh

6. Count the number of mRNA.

grep -i "mRNA" joined.fa

• What other sequences apart from mRNA?

grep "^>" joined.fa | grep -v "mRNA"

• For each category, how many are there?

grep -c "cDNA" joined.fa
grep -c "complete sequence" joined.fa
grep -c "transgenic" joined.fa
grep -c "^>" joined.fa | grep -v "mRNA" | grep -v "cDNA" |grep -v "transgenic" |grep -v "complete sequence"

• Save the above output to files.

grep "cDNA" joined.fa > cDNA.txt
grep "mRNA" joined.fa > mRNA.txt
grep "transgenic" joined.fa > transgenic.txt
grep "complete sequence" joined.fa > complete_sequence.txt

7. How many organisms (create a file with the organisms without duplicates)

grep "PREDICTED" joined.fa | cut -d' ' -f3,4 | uniq -d > organism.txt

8. How many are predicted?

grep -c "PREDICTED"  joined.fa

9. How many nucleotides are in the file? How many of each of the bases are there?

grep -v '^>' sequences.fasta | tr -d '\n' | grep -o '[ACGTU]' | sort | uniq -c