INNER CODE UNIT · Python

prepare_exons_for_cesar

hillerlab/TOGA · CESAR_wrapper.py:506

def prepare_exons_for_cesar(exon_seqs):
    """Cesar requires some special formatting for exons."""
    # CESAR requires a special king of reference exons formatting
    # Split codons should be written in lowercase, as follows:
    # ATGTTTa ctGTAAAGTGCc ttAGTTGA
    verbose("prepare_exons_for_cesar")
    left_pointer = 0  # init value
    cesar_input_exons = {}  # accumulate result here

    for k, exon_seq in exon_seqs.items():
        # define number of letters to lowercase at the right side
        right_pointer = (len(exon_seq) - left_pointer) % 3
        # apply left pointer
        if left_pointer != 3:  # it it were accumulated 3 bases it has no sense like 0
            exon_seq_lfix = (
                exon_seq[:left_pointer].lower() + exon_seq[left_pointer:].upper()
            )
        else:  # don't touch if left_pointer == 0 or == 3

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