This repository contains the assignment on Introduction to Linux
- Create a project directory called Exercise. Which commands did you use?
#creating a directory using mkdir command
mkdir Exercise
- In the directory, create all the sub-directories you would need for a Bioinformatics Project
cd Exercise
mkdir -p data scripts results
- With the provided dataset files, put them in the appropriate directories you created under your Bioinformatics Project
#Using the mv command to move the datasets from downloads folder to data folder
cd data
mv ../nrf1_seq* ./
- Extract the sequence headers and save into a file
sequence_names.txtin the appropriate directory
#Extracting sequence headers using grep
grep "^>" nrf1_seq.fa >> ../results/sequence_names.txt
grep "^>" nrf1_seqtemp.fa >> ../results/sequence_names.txt
- Save the commands you used in question 4 in a script file
extract_seq.sh
nano extract_seq.sh
#!/usr/bin/bash
#Commands to extract sequence headers from a fasta file
grep "^>" nrf1_seq.fa >> ../results/sequence_names.txt
grep "^>" nrf1_seqtemp.fa >> ../results/sequence_names.txt
- Count the number of mRNA.
grep -c "mRNA" nrf1_seq.fa
#Output : 90
grep -c "mRNA" nrf1_seqtemp.fa
#Output : 90
- What other sequences apart from mRNA?
cDNA
- For each category, how many are there?
grep -v "mRNA" sample_headers.txt |wc
#output : 20
- Save the above output to files.
grep -v "mRNA" sample_headers.txt > non_mrna.txt
- How many organisms (create a file with the organisms without duplicates)
#Extracting organisms and saving in file species.txt
grep ">" sequence_names.txt | cut -d, -f1 | sed 's/PREDICTED://g' | awk '{print $2,$3}' >> species.txt
#Counting unique species
sort species.txt | uniq |wc
#Output : 36 unique organisms
- How many are predicted?
grep -c "PREDICTED" sequence_names.txt
#Output : 156
- How many nucleotides are in the file? How many of each of the bases are there?
#Number of nucleotides in nrf1_seq fasta file
#First I extract only the nucleotides and save them in a new file using grep -v
grep -v "^>" nrf1_seq.fa > nrf1_seq
#Then filter out the last line doesnt contain a valid nucleotide
head -n -1 nrf1_seq > nrf1.seq
#Counting number of nucleotides using wc -m flag which counts characters
wc -m nrf1.seq
#Output : 820493
- Number of nucleotides in nrf1_seqtemp.fa
grep -v "^>" nrf1_seqtemp.fa |wc -m
#Output: 820493
- Number of each bases
#Counting each number of nucleotide using grep -o flag which show only nonempty parts of lines that match.
#Count of A
grep -o 'A' nrf1_seqtemp |wc -l
#output:215395
#Count of G
grep -o 'G' nrf1_seqtemp |wc -l
#Output: 193881
#Count of C
grep -o 'C' nrf1_seqtemp |wc -l
#output:184571
#Count of T
grep -o 'T' nrf1_seqtemp |wc -l
#Output: 216465