def test_get_exon_ranges_03():
"get_exon_ranges() test."
genbank_txt = utilslib.read_file('genbank/lysozyme-3-bos-taurus.gbff')
res = e2.get_exon_ranges(genbank_txt)
ref = [(1, 144), (144, 309), (309, 385), (385, 950)]
assert res == ref
def test_get_exon_ranges_02():
"get_exon_ranges() test."
genbank_txt = utilslib.read_file('genbank/lysozyme-1-mus-musculus.gbff')
res = e2.get_exon_ranges(genbank_txt)
ref = [(0, 166), (166, 331), (331, 410), (410, 1265)]
assert res == ref
def test_get_exon_ranges_01():
"get_exon_ranges() test: exon keyword outside of FEATUES TRAP."
genbank_txt = utilslib.read_file('genbank/lysozyme-3-bos-taurus-trap.gbff')
res = e2.get_exon_ranges(genbank_txt)
ref = [(1, 144), (144, 309), (309, 385), (385, 950)]
assert res == ref
def test_get_exon_ranges_04():
"get_exon_ranges() test."
genbank_txt = utilslib.read_file(
'genbank/lysozyme-p-drosophila-melanogaster.gbff')
res = e2.get_exon_ranges(genbank_txt)
ref = []
assert res == ref
def test_get_dna_seq_04():
"get_dna_seq() test."
filename = 'lysozyme-p-drosophila-melanogaster'
genbank_txt = utilslib.read_file(f'genbank/{filename}.gbff')
res = e1.get_dna_seq(genbank_txt)
ref = utilslib.read_fasta(f'fasta/{filename}.fasta')[0]
assert res == ref
def test_get_dna_seq_03():
"get_dna_seq() test."
filename = 'lysozyme-3-bos-taurus'
genbank_txt = utilslib.read_file(f'genbank/{filename}.gbff')
res = e1.get_dna_seq(genbank_txt)
ref = utilslib.read_fasta(f'fasta/{filename}.fasta')[0]
assert res == ref
def test_get_dna_seq_01():
"get_dna_seq() test."
filename = 'insulin-h**o-sapiens'
genbank_txt = utilslib.read_file(f'genbank/{filename}.gbff')
res = e1.get_dna_seq(genbank_txt)
ref = utilslib.read_fasta(f'fasta/{filename}.fasta')[0]
assert res == ref
def main(genbank_filename_in: str, fasta_filename_out):
"""Reads genbank_filename_in and writes its exons into fasta_filename_in.
- Each exon starts with a comment line like this: >exon
- Each exon is separated by a blank line from other exons.
- The last exon does not have any whitespace nor newlines at the end.
"""
genbank_txt = utilslib.read_file(genbank_filename_in)
exons = get_exons(genbank_txt)
fasta_str = make_exons_fasta_str(exons)
utilslib.write_file(fasta_str, fasta_filename_out)