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Final exam Di Lena. Module 3 version 7
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- The document presents a shell scripting exam focused on bioinformatics applications.
- It includes a sample dataset named
fastq.txt, structured similarly to a FASTQ file, containing sequence identifiers, nucleotide sequences, and quality scores. This dataset is central to all the practical exercises. - Question 1 (2 points) involves analyzing two slightly different pipelines of commands:
cat fastq.txt | sort | cut -c 1-11 | tail -4 | uniq | wc -1cat fastq.txt | cut -c 1-11 | sort | tail -4 | uniq | wc -1- This question specifically tests the impact of command order (
sortbeforecutvs.cutbeforesort) on the final output, as well as the functionality oftail,uniq, andwc -lfor data manipulation and counting.
- Question 2 (2 points) requires determining the output of the command:
cat fastq.txt | grep "@.*6" | wc -l. This problem evaluates the ability to usegrepfor advanced pattern matching (finding lines with '@' followed by any characters and then '6') and then counting these lines usingwc -l. - Question 3 (3 points) focuses on interpreting a more complex
awkscript:cat fastq.txt | awk '$1 /^@/{if(!a[$1]) {a[$1]=1; n++;}}END{print n}'. This command is designed to identify and count the number of unique sequence identifiers (lines starting with '@') within thefastq.txtfile, demonstrating proficiency in usingawkfor data processing, conditional logic, and array management. - Question 4 (3 points) asks for the output of:
cat fastq.txt | sed '/^@/d' | wc -l. This exercise assesses the understanding ofsedfor deleting specific lines (those starting with '@') and then usingwc -lto count the total number of remaining lines after the deletion. - Collectively, these exercises are designed to evaluate a student's practical skills in using common Unix shell commands and scripting for tasks relevant to bioinformatics data processing, such as filtering, sorting, extracting, and counting specific elements within large text-based datasets.