Bam Records to Fasta

bam_to_fasta.py

from pbcore.io import FastaReader, BamReader

def to_records(reader_klass, transform_func, file_name):
    with reader_klass(file_name) as r:
        for record in r:
            yield transform_func(record)

def bam_record_to_fasta_record(b_record):
    # fill me in here
    return b_record


def bam_or_fasta(file_name):
    reader = FastaReader
    t_func = lambda x: x
    if file_name.endswith(".bam"):
        reader = BamReader
        t_func = bam_record_to_fasta_record
    return to_records(reader, t_func, file_name)