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import gffutils
from textwrap import dedent
TEST_FILENAMES = [
gffutils.example_filename(i)
for i in [
"c_elegans_WS199_ann_gff.txt",
"ensembl_gtf.txt",
"hybrid1.gff3",
"ncbi_gff3.txt",
"c_elegans_WS199_dna_shortened.fa",
"F3-unique-3.v2.gff",
"jgi_gff2.txt",
"wormbase_gff2_alt.txt",
"c_elegans_WS199_shortened_gff.txt",
"glimmer_nokeyval.gff3",
"mouse_extra_comma.gff3",
"wormbase_gff2.txt",
]
]
def parser_smoke_test():
"""
Just confirm we can iterate completely through the test files....
"""
# Don't show the warnings for tests
import logging
gffutils.parser.logger.setLevel(logging.CRITICAL)
for filename in TEST_FILENAMES:
p = gffutils.iterators._FileIterator(filename)
for i in p:
continue
def test_file_iterator():
db = gffutils.create_db(gffutils.example_filename("hybrid1.gff3"), ":memory:")
n = len(list(db.all_features()))
assert n == 6, n
def test_feature_iterator():
it = gffutils.DataIterator(gffutils.example_filename("hybrid1.gff3"))
# A DataIterator of a _FileIterator should be a _FeatureIterator
it = gffutils.DataIterator((i for i in it))
assert isinstance(it, gffutils.iterators._FeatureIterator), it
it = gffutils.DataIterator(it)
db = gffutils.create_db(it, ":memory:")
n = len(list(db.all_features()))
assert n == 6, n
def test_update():
db = gffutils.create_db(
gffutils.example_filename("FBgn0031208.gtf"),
":memory:",
disable_infer_genes=True,
)
f = gffutils.feature.feature_from_line(
'chr2L gffutils_derived gene 11500 12500 . - . gene_id "fake";', strict=False
)
db.update([f], disable_infer_genes=True)
for i in db.all_features():
print(i.id)
assert f == db["fake"]
def test_string_iterator():
gtfdata = dedent(
"""
chr1 a testing 1 10 . + . gene_id "fake"; n "2";
chr1 b testing 1 10 . + . gene_id "fake"; n "1";
"""
)
data = gffutils.iterators.DataIterator(gtfdata, from_string=True)
n = len(list(data))
assert n == 2, n
db = gffutils.create_db(gtfdata, ":memory:", from_string=True)
n = len(list(db.all_features()))
assert n == 2, n
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