Dee Dee Dev‐Diary - TheEvergreenStateCollege/bioinformatics GitHub Wiki

Week 01

Time

2024-04-05 Meeting: 2.5 hrs

2024-04-06 Research: 2.0 hrs

2024-04-07 Research/Programming: 3.0 hrs

TODO

Research Topics Week 01

Rust Programming Language: Syntax and semantics of Rust programming language. Basic concepts like functions, structs, error handling, traits, etc. Usage of standard library modules like std::fs::File, std::io, std::env, etc.

TOML: TOML syntax and its common use cases. Parsing TOML files in Rust using libraries like... toml.

FASTA Format: Understanding the FASTA format for biological sequence data. Parse and handle FASTA-formatted files in Rust. Understand the basic differences between DNA and RNA.

Command-Line Arguments Handling: Parsing command-line arguments in Rust using std::env::args. Checking and processing command-line arguments passed to the program.

Error Handling in Rust: Rust's error handling mechanisms using Result and Option. Implementing custom error types and handling different error scenarios.

File I/O Operations: Reading from and writing to files in Rust using std::fs::File and related modules. Using BufReader for reading of file contents line by line.

Itertools Crate: Functionality provided by the itertools crate in Rust. Combinations method to generate combinations of elements from a collection.

Serde Crate: Working with the serde crate for serialization and deserialization of data structures in Rust. Serialize and Deserialize trait and its usage.

Weight Calculation Logic: Understanding how weights are calculated based on character and token matching between sequences.

Graph Theory Concepts: Graphs and graph edges refresher. Generating edges between sequences based on their weights.