rocketfasta 🚀

Overview

The FASTA Parser is a command-line tool designed to process FASTA files, retrieve sequence headers, and extract sequences based on a specified reference ID.

Command-line Arguments

1. Input File (-i, --fasta-input)

• Description: Specifies the path to the input FASTA file.
• Usage: This argument is required for the program to run.
• Syntax:

  -i <path_to_file> 
  --fasta-input <path_to_file>

• Example:

  ./fasta_parser -i input.fasta

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2. Print Headers (-H, --print-headers)

• Description: A flag to print the headers of the FASTA sequences. When this option is specified, the program will display the headers from the input FASTA file.
• Usage: This argument is optional and acts as a flag (no additional value required).
• Syntax:

  -H 
  --print-headers

• Example:

  ./fasta_parser -i input.fasta -H

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3. Reference ID (-r, --reference-id)

• Description: Specifies the ID of the reference sequence to be located in the FASTA file. The program will search for and operate on the sequence with the given reference ID.
• Usage: This argument is optional but requires a string value corresponding to the reference ID.
• Syntax:

  -r <reference_id>
  --reference-id <reference_id>

• Example:

  ./fasta_parser -i input.fasta -r ref123

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4. Se (-s, --subsequence-pattern)

• Description: "A nucleotide sequence that you want to file in the fasta sequences of fasta file. Return BED style Start and End coordinates.
• Usage: This argument is optional but requires a string value corresponding to the wanted subsequence to be searched.
• Syntax:

  -s <nucleotide_sequence> 
  --subsequence-pattern <nucleotide_sequence>

• Example:

  ./fasta_parser -i input.fasta -s ATGT

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Usage Examples

Example 1: Parse a FASTA file and print all headers

./fasta_parser -i input.fasta -H

Example 2: Parse a FASTA file and find aligns the sequence with the ID provided to the other sequences in file.

./fasta_parser -i input.fasta -r ID_123

Example 3: Parse a FASTA file without additional options

./fasta_parser -i input.fasta

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Exit Codes

• 0: Program executed successfully.
• 1: Missing required arguments or invalid input.

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Notes

• The input file must be in valid FASTA format.
• The program ensures UTF-8 compliance for all input arguments.

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Credits

Developed using the CLI11 library.