scallops.io.read_barcodes

scallops.io.read_barcodes(barcodes_path, barcode_indices, barcode_column='barcode')

Load barcodes from a CSV file.

This function reads barcodes from a CSV file. It optionally allows selecting specific indices from the barcode column. It performs validation to ensure all barcodes have the same length.

Parameters:

• barcodes_path (str) – Path to the CSV file containing barcodes.

• barcode_indices (None | Sequence[int]) – Optional list of indices (0-based) to extract from the barcode column.

• barcode_column (str) – Name of the barcode column in the CSV file.

Returns:

DataFrame containing the loaded barcodes.

Example:

Return type:

DataFrame

import scallops.io

# Define the path to the barcodes CSV file
barcodes_path = "path/to/barcodes.csv"

# Load barcodes without selecting specific indices
barcodes_df = scallops.io.read_barcodes(barcodes_path)
print(barcodes_df.head())

# Load barcodes and select specific indices
selected_indices = [0, 1, 2]
barcodes_df_selected = scallops.io.read_barcodes(
    barcodes_path, barcode_indices=selected_indices
)
print(barcodes_df_selected.head())