def test_find_match_with_diff_5(self):
""" Example of an ISM where the start is different from the match
"""
conn, cursor = get_db_cursor()
build = "toy_build"
transcript_dict = talon.make_transcript_dict(cursor)
edges = ( 200, 13, 14 )
gene_ID, transcripts = talon.search_for_transcript_prefix(edges, transcript_dict)
# Make sure that correct match got returned
correct_gene_ID = fetch_correct_ID("TG2", "gene", cursor)
assert gene_ID == correct_gene_ID
conn.close()
def test_find_no_match(self):
""" Example where the toy transcript database contains no matches
for the edge set.
"""
conn, cursor = get_db_cursor()
build = "toy_build"
transcript_dict = talon.make_transcript_dict(cursor)
conn.close()
edges = (1, 2, 3)
gene_ID, transcripts = talon.search_for_transcript_suffix(
edges, transcript_dict)
# Make sure that no match got returned
assert gene_ID == None
def test_find_monoexon_match(self):
""" Input is a single exon that matches the end of an existing transcript
"""
conn, cursor = get_db_cursor()
build = "toy_build"
transcript_dict = talon.make_transcript_dict(cursor)
edges = (16, )
gene_ID, matches = talon.search_for_transcript_suffix(
edges, transcript_dict)
# Make sure that correct match got returned
correct_gene_ID = fetch_correct_ID("TG2", "gene", cursor)
assert gene_ID == correct_gene_ID
conn.close()
def test_find_match(self):
""" Example where the toy transcript database contains exactly one
prefix match for the transcript.
"""
conn, cursor = get_db_cursor()
build = "toy_build"
transcript_dict = talon.make_transcript_dict(cursor)
edges = ( 12, 13, 14 )
gene_ID, transcripts = talon.search_for_transcript_prefix(edges, transcript_dict)
# Make sure that correct match got returned
correct_gene_ID = fetch_correct_ID("TG2", "gene", cursor)
assert gene_ID == correct_gene_ID
assert transcripts == [(12, 13, 14, 15, 16)]
conn.close()