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Final exam Di Lena. Module 3 version 5
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- This document outlines a series of shell scripting exercises designed for bioinformatics students.
- The core task involves processing a simulated dataset, `casp13.txt`, which contains protein sequence information.
- The `casp13.txt` file includes data points such as:
- Header lines (starting with `>`) with identifiers (e.g., `H0974`, `Q3KP22-3`).
- Source information (e.g., `048503/048504`, `Human`, `E. coli`).
- Subunit details and residue counts.
- Actual protein sequences.
- The exercises require the application of various Unix command-line utilities in pipelines:
- `cat`: To display file content.
- `sort`: For sorting lines alphabetically or numerically.
- `cut`: To extract specific columns or character ranges.
- `head`: To output the first part of files.
- `wc`: To count lines, words, and characters.
- `grep`: For searching text using patterns (including regular expressions).
- `awk`: A powerful pattern-scanning and processing language, used here for field extraction and conditional printing.
- `sed`: A stream editor for filtering and transforming text, used for deleting lines based on patterns.
- Specific questions challenge students to:
- Determine the count of unique prefixes from sorted protein data after truncating lines.
- Count specific header lines containing a particular digit.
- Extract and count unique identifiers from header lines using `awk`.
- Calculate the total number of sequence lines after removing header and specific sequence lines using `sed`.
- These exercises are fundamental for developing skills in data manipulation, pattern matching, and building efficient command-line workflows essential for bioinformatics research.
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