csv

CSVParser Class

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Overview

The CSVParser class is designed to parse CSV files containing biological sequence data (DNA, RNA, or Protein) and convert them into corresponding Python objects (DNA, RNA, or Protein). It leverages the pandas library to read and process CSV files, making it easy to handle large datasets efficiently.

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Class Definition

class CSVParser:
    def __init__(self, file_path):
        """
        Initialize a new CSVParser object.
        :param file_path: Path to the CSV file containing biological sequence data
        """
        ...

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Attributes

Attribute	Type	Description
file_path	str	Path to the CSV file.
data	pandas.DataFrame	DataFrame containing the parsed CSV data.

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Methods

Initialization

• __init__(self, file_path) Initializes a new CSVParser instance with the specified CSV file path. The CSV file is read into a pandas.DataFrame for further processing.

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Parsing Records

• parse_records(self) -> List[Union[DNA, RNA, Protein]] Parses the CSV data and converts each row into the appropriate biological object (DNA, RNA, or Protein).

  • Returns: A list of parsed biological objects (DNA, RNA, or Protein).

  • Details:

    • Iterates over each row in the CSV file.
    • Determines the type of sequence (DNA, RNA, or Protein) based on the type column.
    • Creates the corresponding object and appends it to the result list.

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CSV File Format

The CSV file should have the following columns:

Column Name	Description
sequence	The biological sequence (e.g., "ATGC" for DNA, "AUG" for RNA, "ACDEF" for Protein).
type	The type of sequence (DNA, RNA, or Protein).
id	(Optional) Unique identifier for the sequence (required for Protein objects).

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Example Usage

CSV File Example (sequences.csv)

sequence,type,id
ATGCGATCG,DNA,
AUGCCGUA,RNA,
ACDEFGHIKLMNPQRSTVWY,Protein,Protein1

Python Code Example

# Initialize the CSVParser with the path to the CSV file
parser = CSVParser(file_path="sequences.csv")

# Parse the records
parsed_elements = parser.parse_records()

# Print the parsed elements
for element in parsed_elements:
    print(element)

Expected Output

DNA Sequence: ATGCGATCG
RNA Sequence: AUGCCGUA
Protein: Protein1, Sequence: ACDEFGHIKLMNPQRSTVWY

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Dependencies

• pandas: Used for reading and processing CSV files.
• DNA: Class representing DNA sequences.
• RNA: Class representing RNA sequences.
• Protein: Class representing protein sequences.

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Error Handling

• If the CSV file does not contain the required columns (sequence, type), the CSVParser will raise a KeyError.
• If the type column contains an invalid value (not DNA, RNA, or Protein), the corresponding row will be skipped.

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Notes

• The CSVParser class is designed to be flexible and can be extended to support additional biological sequence types or custom parsing logic.
• The id column is optional and only required for Protein objects. If not provided, the Protein constructor should handle it appropriately.

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