CodonU.extractor

Submodules

Package Contents

Functions

extract_cds_lst(→ tuple[Any, Ellipsis])

Extracts the list of features if their type is CDS

extract_cds(→ Bio.SeqRecord.SeqRecord)

Returns the CDS as a Sequence Record object

extract_prot

extract_exome

CodonU.extractor.extract_cds_lst(record: Bio.SeqRecord.SeqRecord) → tuple[Any, Ellipsis]

Extracts the list of features if their type is CDS

Parameters:

record – Original Sequence Record object from where the CDS is to be extracted

Returns:

A tuple of FeatureLocation objects

CodonU.extractor.extract_cds(record: Bio.SeqRecord.SeqRecord, cds_feature: Bio.SeqFeature.SeqFeature) → Bio.SeqRecord.SeqRecord

Returns the CDS as a Sequence Record object

Parameters:

  • record – Original Sequence Record object from where the CDS is to be extracted

  • cds_feature – Sequence Feature object of corresponding SeqRecord object

Returns:

The new Sequence Record object containing the CDS

CodonU.extractor.extract_prot(feature: Bio.SeqFeature.SeqFeature, organism_name: str) → Bio.SeqRecord.SeqRecord

Extracts protein sequences and return them for writing

Parameters:

  • feature – The CDS

  • organism_name – Name of the organism

  • cds_no – Number of the CDS

Returns:

The protein sequence suitable for being written is fasta format

CodonU.extractor.extract_exome(records: list[Bio.SeqRecord.SeqRecord], exclude_stops: bool = True) → Bio.SeqRecord.SeqRecord

Extracts the exome from given nucleotides :param records: List of SeqRecord objects containing each CDS :param exclude_stops: If true, intermediate stops codons are excluded from exome :return: The exome