def test_random_chr():
"""
Test on GFF files with random chromosome events.
"""
gff_fname = gffutils.example_filename("random-chr.gff")
db = helpers.get_gff_db(gff_fname)
# Test that we can get children of only a selected type
gene_id = \
"chr1_random:165882:165969:-@chr1_random:137473:137600:-@chr1_random:97006:97527:-"
mRNAs = db.children(gene_id, featuretype="mRNA")
for mRNA_entry in mRNAs:
assert (mRNA_entry.featuretype == "mRNA"), \
"Not all entries are of type mRNA! %s" \
%(",".join([entry.featuretype for entry in mRNAs]))
print("Parsed random chromosome successfully.")
def test_random_chr():
"""
Test on GFF files with random chromosome events.
"""
gff_fname = gffutils.example_filename("random-chr.gff")
db = helpers.get_gff_db(gff_fname)
# Test that we can get children of only a selected type
gene_id = \
"chr1_random:165882:165969:-@chr1_random:137473:137600:-@chr1_random:97006:97527:-"
mRNAs = db.children(gene_id, featuretype="mRNA")
for mRNA_entry in mRNAs:
assert (mRNA_entry.featuretype == "mRNA"), \
"Not all entries are of type mRNA! %s" \
%(",".join([entry.featuretype for entry in mRNAs]))
print("Parsed random chromosome successfully.")
def test_sanitize_gff():
"""
Test sanitization of GFF. Should be merged with GFF cleaning
I believe unless they are intended to have different functionalities.
"""
# Get unsanitized GFF
fn = gffutils.example_filename("unsanitized.gff")
# Get its database
db = helpers.get_gff_db(fn)
# Sanitize the GFF
sanitized_recs = helpers.sanitize_gff_db(db)
# Ensure that sanitization work, meaning all
# starts must be less than or equal to stops
for rec in sanitized_recs.all_features():
assert (rec.start <= rec.stop), "Sanitization failed."
print("Sanitized GFF successfully.")
def test_sanitize_gff():
"""
Test sanitization of GFF. Should be merged with GFF cleaning
I believe unless they are intended to have different functionalities.
"""
# Get unsanitized GFF
fn = gffutils.example_filename("unsanitized.gff")
# Get its database
db = helpers.get_gff_db(fn)
# Sanitize the GFF
sanitized_recs = helpers.sanitize_gff_db(db)
# Ensure that sanitization work, meaning all
# starts must be less than or equal to stops
for rec in sanitized_recs.all_features():
assert (rec.start <= rec.stop), "Sanitization failed."
print("Sanitized GFF successfully.")
