def setUp(self):
self.ticket1 = ticket.ImportTicket()
self.src1 = source.Source()
self.src1.id = "L5_SRC_1"
self.src2 = source.Source()
self.src2.id = "L5_SRC_2"
self.src3 = source.Source()
self.src3.id = "L5_SRC_3"
self.cds1 = cds.Cds()
self.cds1.id = "L5_CDS_1"
self.cds2 = cds.Cds()
self.cds2.id = "L5_CDS_2"
self.cds3 = cds.Cds()
self.cds3.id = "L5_CDS_3"
self.trna1 = trna.Trna()
self.trna1.id = "L5_TRNA_1"
self.trna2 = trna.Trna()
self.trna2.id = "L5_TRNA_2"
self.trna3 = trna.Trna()
self.trna3.id = "L5_TRNA_3"
self.tmrna1 = tmrna.Tmrna()
self.tmrna1.id = "L5_TMRNA_1"
self.tmrna2 = tmrna.Tmrna()
self.tmrna2.id = "L5_TMRNA_2"
self.tmrna3 = tmrna.Tmrna()
self.tmrna3.id = "L5_TMRNA_3"
self.genome1 = genome.Genome()
self.genome1.type = "flat_file"
self.genome1.cds_features = [self.cds1, self.cds2]
self.genome1.source_features = [self.src1, self.src2]
self.genome1.trna_features = [self.trna1, self.trna2]
self.genome1.tmrna_features = [self.tmrna1, self.tmrna2]
self.genome2 = genome.Genome()
self.genome2.type = "mysql"
self.genome_pair1 = genomepair.GenomePair()
self.genome_pair2 = genomepair.GenomePair()
self.bndl = bundle.Bundle()
self.bndl.ticket = self.ticket1
self.bndl.genome_dict[self.genome1.type] = self.genome1
self.bndl.genome_dict[self.genome2.type] = self.genome2
self.bndl.genome_pair_dict["genome_pair1"] = self.genome_pair1
self.bndl.genome_pair_dict["genome_pair2"] = self.genome_pair2
self.eval_correct1 = evaluation.Evaluation(status="correct")
self.eval_correct2 = evaluation.Evaluation(status="correct")
self.eval_error1 = evaluation.Evaluation(status="error")
self.eval_error2 = evaluation.Evaluation(status="error")
def setUp(self):
self.feature = tmrna.Tmrna()
self.seq1 = Seq("AATTCGAGCT")
self.seqfeature1 = test_data_utils.create_1_part_seqfeature(
1, 5, 1, "CDS")
self.seqfeature2 = test_data_utils.create_1_part_seqfeature(
1, 5, -1, "CDS")
self.seqfeature3 = test_data_utils.create_2_part_seqfeature(
1, 5, 1, 3, 7, 1, "CDS")
def test_create_tmrna_table_insert_1(self):
"""Verify tmrna table INSERT statement is created correctly when
locus_tag, note, and peptide_tag are not empty."""
# Note: even though this function returns a string and doesn't
# actually utilize a MySQL database, this test ensures
# that the returned statement will function properly in MySQL.
tmrna1 = tmrna.Tmrna()
tmrna1.id = "Trixie_1"
tmrna1.genome_id = "Trixie"
tmrna1.name = "1"
tmrna1.locus_tag = "TAG1"
tmrna1.start = 5
tmrna1.stop = 10
tmrna1.length = 200
tmrna1.orientation = "F"
tmrna1.note = "misc"
tmrna1.peptide_tag = "random"
statement = mysqldb.create_tmrna_table_insert(tmrna1)
test_db_utils.execute(statement)
result = test_db_utils.get_data(TMRNA_QUERY2)
results = result[0]
exp = ("""INSERT INTO tmrna """
"""(GeneID, PhageID, Start, Stop, Length, """
"""Name, Orientation, Note, LocusTag, PeptideTag) """
"""VALUES """
"""("Trixie_1", "Trixie", 5, 10, 200, """
""""1", "F", "misc", "TAG1", "random");""")
with self.subTest():
self.assertEqual(statement, exp)
with self.subTest():
self.assertEqual(results["GeneID"], "Trixie_1")
with self.subTest():
self.assertEqual(results["PhageID"], "Trixie")
with self.subTest():
self.assertEqual(results["Start"], 5)
with self.subTest():
self.assertEqual(results["Stop"], 10)
with self.subTest():
self.assertEqual(results["Length"], 200)
with self.subTest():
self.assertEqual(results["Name"], "1")
with self.subTest():
self.assertEqual(results["Orientation"], "F")
with self.subTest():
self.assertEqual(results["Note"].decode("utf-8"), "misc")
with self.subTest():
self.assertEqual(results["LocusTag"], "TAG1")
with self.subTest():
self.assertEqual(results["PeptideTag"], "random")
def parse_tmrna_seqfeature(seqfeature):
"""
Parses data from a BioPython tmRNA SeqFeature object into a
Tmrna object.
:param seqfeature: BioPython SeqFeature
:type seqfeature: SeqFeature
:return: pdm_utils Tmrna object
:rtype: Tmrna
"""
tmrna_ftr = tmrna.Tmrna()
tmrna_ftr.seqfeature = seqfeature
try:
locus_tag = seqfeature.qualifiers["locus_tag"][0]
except (KeyError, IndexError):
locus_tag = ""
finally:
tmrna_ftr.set_locus_tag(locus_tag, delimiter=None)
tmrna_ftr.set_orientation(seqfeature.strand, "fr_short", True)
tmrna_ftr.start, tmrna_ftr.stop, tmrna_ftr.parts = parse_coordinates(
seqfeature)
# Coordinate format for GenBank flat file features parsed by Biopython
# are 0-based half open intervals.
tmrna_ftr.coordinate_format = "0_half_open"
tmrna_ftr.set_nucleotide_length(use_seq=True)
try:
note = seqfeature.qualifiers["note"][0]
except (KeyError, IndexError):
note = ""
finally:
tmrna_ftr.note = note
try:
gene = seqfeature.qualifiers["gene"][0]
except (KeyError, IndexError):
gene = ""
finally:
tmrna_ftr.gene = gene
tmrna_ftr.set_name()
return tmrna_ftr
def parse_tmrna_table_data(data_dict):
"""Parse a MySQL database dictionary to create a Tmrna object.
:param data_dict:
Dictionary of data retrieved from the gene table.
:type data_dict: dict
:returns: A pdm_utils Tmrna object.
:rtype: Tmrna
"""
ftr = tmrna.Tmrna()
ftr.type = "tmRNA"
try:
ftr.id = data_dict["GeneID"]
except:
pass
try:
ftr.genome_id = data_dict["PhageID"]
except:
pass
try:
ftr.start = int(data_dict["Start"])
except:
pass
try:
ftr.stop = int(data_dict["Stop"])
except:
pass
try:
ftr.length = int(data_dict["Length"])
except:
pass
try:
ftr.name = data_dict["Name"]
except:
pass
try:
ftr.orientation = data_dict["Orientation"]
except:
pass
try:
ftr.set_locus_tag(data_dict["LocusTag"])
except:
pass
try:
ftr.note = data_dict["Note"].decode("utf-8")
except:
pass
try:
ftr.peptide_tag = data_dict["PeptideTag"]
except:
pass
try:
ftr.parts = 1
except:
pass
ftr.coordinate_format = "0_half_open"
return ftr
def setUp(self):
self.genome1 = genome.Genome()
self.genome1.id = "L5"
self.genome1.name = "L5_Draft"
self.genome1.host_genus = "Mycobacterium"
self.genome1.annotation_status = "final"
self.genome1.accession = "ABC123"
self.genome1.seq = "ATCG"
self.genome1.length = 4
self.genome1.gc = 0.5001
self.genome1.date = '1/1/2000'
self.genome1.retrieve_record = "1"
self.genome1.annotation_author = "1"
self.genome1.cluster = "A"
self.genome1.subcluster = "A2"
self.cds1 = cds.Cds()
self.cds1.genome_id = "L5"
self.cds1.start = 10
self.cds1.stop = 100
self.cds1.parts = 1
self.cds1.length = 1000
self.cds1.name = "1"
self.cds1.type = "CDS"
self.cds1.translation = "AGGPT"
self.cds1.orientation = "F"
self.cds1.description = "description"
self.cds1.locus_tag = "SEA_L5_001"
self.cds2 = cds.Cds()
self.cds2.genome_id = "L5"
self.cds2.start = 100
self.cds2.stop = 1000
self.cds2.parts = 1
self.cds2.length = 10000
self.cds2.name = "2"
self.cds2.type = "CDS"
self.cds2.translation = "AKKQE"
self.cds2.orientation = "R"
self.cds2.description = "description"
self.cds2.locus_tag = "SEA_L5_002"
self.cds_features = [self.cds1, self.cds2]
self.trna1 = trna.Trna()
self.trna1.id = "Trixie_1"
self.trna1.genome_id = "Trixie"
self.trna1.name = "1"
self.trna1.locus_tag = "TAG1"
self.trna1.start = 5
self.trna1.stop = 10
self.trna1.length = 200
self.trna1.orientation = "F"
self.trna1.note = "misc"
self.trna1.amino_acid = "Ala"
self.trna1.anticodon = "AAA"
self.trna1.structure = "random"
self.trna1.use = "aragorn"
self.trna2 = trna.Trna()
self.trna2.id = "Trixie_1"
self.trna2.genome_id = "Trixie"
self.trna2.name = "1"
self.trna2.locus_tag = "TAG1"
self.trna2.start = 5
self.trna2.stop = 10
self.trna2.length = 200
self.trna2.orientation = "F"
self.trna2.note = "misc"
self.trna2.amino_acid = "Ala"
self.trna2.anticodon = "AAA"
self.trna2.structure = "random"
self.trna2.use = "aragorn"
self.trna_features = [self.trna1, self.trna2]
self.tmrna1 = tmrna.Tmrna()
self.tmrna1.id = "Trixie_1"
self.tmrna1.genome_id = "Trixie"
self.tmrna1.name = "1"
self.tmrna1.locus_tag = "TAG1"
self.tmrna1.start = 5
self.tmrna1.stop = 10
self.tmrna1.length = 200
self.tmrna1.orientation = "F"
self.tmrna1.note = "misc"
self.tmrna1.peptide_tag = "random"
self.tmrna2 = tmrna.Tmrna()
self.tmrna2.id = "Trixie_1"
self.tmrna2.genome_id = "Trixie"
self.tmrna2.name = "1"
self.tmrna2.locus_tag = "TAG1"
self.tmrna2.start = 5
self.tmrna2.stop = 10
self.tmrna2.length = 200
self.tmrna2.orientation = "F"
self.tmrna2.note = "misc"
self.tmrna2.peptide_tag = "random"
self.tmrna_features = [self.tmrna1, self.tmrna2]