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module abstract_classes.sample_processor

Abstract sample processor classes.

Global Variables

  • columns_model

class SampleProcessor

Abstract sample processor class.

Defines methods to process sample records.

Args:

  • records: Pandas DataFrame object.
  • config: Config object.

Attributes:

  • records: Pandas DataFrame object.
  • config: Config object.

method __init__

__init__(
    config: Config,
    records: DataFrame = Empty DataFrame
Columns: [name, source, annotations, reference_sequences, fragment_length_distribution_sd, fragment_length_distribution_mean, read_orientation, star_sjdb_overhang, salmon_kmer_size, paths_1, paths_2, adapter_3p_1, adapter_3p_2, adapter_5p_1, adapter_5p_2, adapter_poly_3p_1, adapter_poly_3p_2, adapter_poly_5p_1, adapter_poly_5p_2, sequencing_mode, assembly, identifier, source_sanitized, type]
Index: []
) → None

Class constructor method.

method process

process() → DataFrame

Process records.