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.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.genome1 = genome.Genome()
self.genome1.type = "flat_file"
self.genome1.cds_features.append(self.cds1)
self.genome1.cds_features.append(self.cds2)
self.genome1.source_features.append(self.src1)
self.genome1.source_features.append(self.src2)
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 = eval.Eval(status="correct")
self.eval_correct2 = eval.Eval(status="correct")
self.eval_error1 = eval.Eval(status="error")
self.eval_error2 = eval.Eval(status="error")
def parse_source_seqfeature(seqfeature):
"""Parses a Biopython Source SeqFeature.
:param seqfeature: Biopython SeqFeature
:type seqfeature: SeqFeature
:param genome_id:
An identifier for the genome in which the seqfeature
is defined.
:type genome_id: str
:returns: A pdm_utils Source object
:rtype: Source
"""
src_ftr = source.Source()
src_ftr.seqfeature = seqfeature
start, stop, parts = parse_coordinates(seqfeature)
src_ftr.start = start
src_ftr.stop = stop
try:
src_ftr.organism = str(seqfeature.qualifiers["organism"][0])
except:
src_ftr.organism = ""
try:
src_ftr.host = str(seqfeature.qualifiers["host"][0])
except:
src_ftr.host = ""
try:
src_ftr.lab_host = str(seqfeature.qualifiers["lab_host"][0])
except:
src_ftr.lab_host = ""
src_ftr.parse_organism()
src_ftr.parse_host()
src_ftr.parse_lab_host()
return src_ftr
def setUp(self):
self.feature = source.Source()
def setUp(self):
self.cds_ftr = cds.Cds()
self.src_ftr = source.Source()
self.gnm = genome.Genome()
