def test_writeGeneDataFile(self):
"""Test writeGeneDataFile"""
lGenes = [Gene('GENE1','seq1',12,600,1),Gene('GENE2','seq2',100,1000,-1)]
GeneDataFile = self.plot.writeGeneDataFile(lGenes,'gene.txt')
self.assertTrue(filecmp.cmp(GeneDataFile,'test-data/gene.txt'))
os.remove('gene.txt')
def test_writeCircosConf(self):
"""Test writeCircosConf"""
lSeqs = [('seq1',20000),('seq2',30000)]
GenomeDataFile = self.plot.writeSeqDataFile(lSeqs, 'genome.txt')
lRegions = [(Region('seq1',100,220,1),Region('seq2',100,220,1)),
(Region('seq1',1200,1300,-1),Region('seq2',1300,1400,1))]
lAlgmts = [('ATGCATGCATGCATGCATGCATGCATGCATGCATGCAGGCATGCATGCATGCATGCATGAATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATATGTGTAGTGAGTCGTCCC',
'ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATGATGTACGATATAGCCCAC'),
('ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAA',
'ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAATGCATGCATGCATGCATGCATGCATGCATGCATGCATGAA')]
lDuplications = [Duplication('seq1',1,5000,'seq2',1,6000,lRegions,lAlgmts)]
SDDataFile = self.plot.writeSegDupDataFile(lDuplications,'segdup.txt')
self.plot.writeCircosConf()
self.assertTrue(filecmp.cmp('circos.conf','test-data/circos.conf'))
lGenes = [Gene('GENE1','seq1',12,600,1),Gene('GENE2','seq2',100,1000,-1)]
GeneDataFile = self.plot.writeGeneDataFile(lGenes,'gene.txt')
lTEs = [Feature('TE1','seq1',1000,2000,1,'TE'),Feature('TE2','seq2',4000,4500,-1,'TE')]
TEDataFile = self.plot.writeTEDataFile(lTEs,'TE.txt')
self.plot.writeCircosConf()
self.assertTrue(filecmp.cmp('circos.conf','test-data/circos2.conf'))
SimilarityDataFile = self.plot.writeSimilarityDataFile(lDuplications,'similarity.txt')
self.plot.writeCircosConf()
self.assertTrue(filecmp.cmp('circos.conf','test-data/circos3.conf'))
os.remove('circos.conf')
def test_writeGeneLinkDataFile(self):
"""Test writeGeneLinkDataFile"""
iDup = Duplication('seq1',5,5000,'seq2',10,5000)
iGene1 = Gene('GENE1','seq1',10,100,1)
iGene2 = Gene('GENE2','seq2',100,190,-1)
lGeneLinks = [GeneLink(dup=iDup,gene1=iGene1,gene2=iGene2)]
GeneLinkDataFile = self.plot.writeGeneLinkDataFile(lGeneLinks,'gene-link.txt')
self.assertTrue(filecmp.cmp(GeneLinkDataFile,'test-data/gene-link.txt'))
os.remove('gene-link.txt')
def test_getCDSAlignment(self):
"""test getCDSAlignment"""
gene1 = Gene('G00001', 'Chr1', 1, 27, 1, [
Transcript('G00001.1', 'Chr1', 1, 27, 1, 'G00001', [
CDS('G00001.1_cds_1', 'Chr1', 1, 6, 1, 'G00001.1'),
CDS('G00001.1_cds_1', 'Chr1', 13, 21, 1, 'G00001.1')
])
])
gene2 = Gene('G00002', 'Chr5', 1, 27, 1, [
Transcript('G00002.1', 'Chr5', 1, 27, 1, 'G00002', [
CDS('G00002.1_cds_1', 'Chr5', 1, 6, 1, 'G00002.1'),
CDS('G00002.1_cds_1', 'Chr5', 13, 27, 1, 'G00002.1')
])
])
gl = GeneLink(
Duplication('Chr1', 1, 58, 'Chr5', 1, 60, [
(Region('Chr1', 1, 58, 1), Region('Chr5', 1, 60, 1))
], [(
'ATGTATTCTATCTCATGTTAATGCTAATACTAGTCATGATCAGATACGATGATGAT--TA',
'ATGTATTCTATCTCATGTTACTGCTAATACTAGTCATGATCAGATACGATGATGATCATA')
]), gene1, gene2)
self.assertEquals(
('ATGTATtctatcTCATGTTAAtgctaa', 'ATGTATtctatcTCATGTTACTGCTAA',
Region('Chr1', 1, 27, 1), Region('Chr5', 1, 27, 1)),
gl.getCDSAlignment())
gene1 = Gene('G00001', 'Chr1', 1, 27, 1, [
Transcript('G00001.1', 'Chr1', 1, 27, 1, 'G00001', [
CDS('G00001.1_cds_1', 'Chr1', 1, 6, 1, 'G00001.1'),
CDS('G00001.1_cds_1', 'Chr1', 13, 21, 1, 'G00001.1')
])
])
gene2 = Gene('G00002', 'Chr5', 27, 60, -1, [
Transcript('G00002.1', 'Chr5', 27, 60, -1, 'G00002', [
CDS('G00002.1_cds_1', 'Chr5', 27, 39, -1, 'G00002.1'),
CDS('G00002.1_cds_1', 'Chr5', 48, 60, -1, 'G00002.1')
])
])
gl = GeneLink(
Duplication('Chr1', 1, 58, 'Chr5', 1, 60, [
(Region('Chr1', 1, 58, -1), Region('Chr5', 1, 60, 1))
], [(
'ATGTATTCTATCTCATGTTAATGCTAATACTAGTCATGATCAGATACGATGATGAG--TA',
'ATGTATTCTATCTCATGTTACTGCTAATACTAGTCATGATCAGATACGATGATGATCATA')
]), gene1, gene2)
self.assertEquals(
('atactagtcatGATCAGATAcgatgaTGAG--TA',
'ATACTAGTCATGAtcagatacGATGATGATCATA', Region(
'Chr1', 1, 32, -1), Region('Chr5', 27, 60, 1)),
gl.getCDSAlignment())
def test_getlGenesFromCoordinates(self):
"""Test getlGenesFromCoordinates"""
gene1 = Gene('G00001','Chr1',23988,24919,-1,[Transcript('G00001.1','Chr1',23988,24919,-1,'G00001',[CDS('G00001.1_cds_1','Chr1',23988,24083, -1, 'G00001.1'),CDS('G00001.1_cds_1','Chr1',24274,24427,-1,'G00001.1'),CDS('G00001.1_cds_1','Chr1',24489,24919,-1,'G00001.1')])])
gene2 = Gene('G00002','Chr1',239880,249190,-1,[Transcript('G00002.1','Chr1',239880,249190,-1,'G00002',[CDS('G00002.1_cds_1','Chr1',239880,240830, -1, 'G00002.1'),CDS('G00002.1_cds_1','Chr1',242740,244270,-1,'G00002.1'),CDS('G00002.1_cds_1','Chr1',244890,249190,-1,'G00002.1')])])
lGenes = [gene1,gene2]
# self.db.deleteAllGenes() TODO
self.db.insertlGenes(lGenes)
self.assertEquals([gene2],self.db.getlGenesFromCoordinates('Chr1',230000,250000))
def test_selectAllGenes(self):
"""Test selectAllGenes"""
gene1 = Gene('G00001','Chr1',23988,24919,-1,[Transcript('G00001.1','Chr1',23988,24919,-1,'G00001',[CDS('G00001.1_cds_1','Chr1',23988,24083, -1, 'G00001.1'),CDS('G00001.1_cds_1','Chr1',24274,24427,-1,'G00001.1'),CDS('G00001.1_cds_1','Chr1',24489,24919,-1,'G00001.1')])])
lGenes = [gene1]
# self.db.deleteAllGenes() TODO
self.db.insertlGenes(lGenes)
self.assertEquals([gene1],self.db.selectAllGenes())
def getlGenesFromCoordinates(self, seqid, start, end):
"""Get genes included in a defined region"""
lGenes = []
dGenes = {}
lTranscripts = []
dTranscripts = {}
lCDS = []
dCDS = {}
cursor = self.conn.execute(
'''select id, seqid, start, end, strand from gene where seqid = \'{}\' and start > {} and end < {} order by start'''
.format(seqid, start, end))
for row in cursor:
dGenes[row[0]] = Gene(row[0], row[1], row[2], row[3], row[4])
if dGenes:
cursor = self.conn.execute(
'''select id, seqid, start,end,strand,gene_id from transcript where seqid = \'{}\' and start > {} and end < {} order by start'''
.format(seqid, start, end))
for row in cursor:
transcript = Transcript(row[0], row[1], row[2], row[3], row[4],
row[5])
if transcript.gene_id in dGenes:
dTranscripts[row[0]] = transcript
if len(dGenes[transcript.gene_id].lTranscripts) > 0:
dGenes[transcript.gene_id].lTranscripts.append(
transcript)
else:
dGenes[transcript.gene_id].lTranscripts = [transcript]
if dTranscripts:
cursor = self.conn.execute(
'''select cds_id, seqid, start,end,strand,transcript_id from cds where seqid = \'{}\' and start > {} and end < {} order by start'''
.format(seqid, start, end))
for row in cursor:
cds = CDS(row[0], row[1], row[2], row[3], row[4], row[5])
if cds.transcript_id in dTranscripts:
if len(dTranscripts[cds.transcript_id].lCDS) > 0:
dTranscripts[cds.transcript_id].lCDS.append(cds)
else:
dTranscripts[cds.transcript_id].lCDS = [cds]
return dGenes.values()
def _parse(self):
"""Parse the gff file"""
dGenes = {}
dTranscripts = {}
dCDS = {}
with open(self.inputGffFile, 'r') as input:
for line in input:
if not re.match('^#', line):
line = line.rstrip('\n')
values = line.split('\t')
if values[2] == 'gene':
id = self._getFeatureTagValue('ID',values[8])
currentGene = Gene(id, values[0], int(values[3]), int(values[4]), self._getStrand(values[6]))
dGenes[id] = currentGene
self.lGenes.append(currentGene)
if values[2] == 'mRNA':
id = self._getFeatureTagValue('ID',values[8])
gene_id = self._getFeatureTagValue('Parent', values[8])
#gene_id = '{}_G'.format(id)
#currentGene = Gene(gene_id, values[0], int(values[3]), int(values[4]), self._getStrand(values[6]))
#dGenes[gene_id] = currentGene
#self.lGenes.append(currentGene)
currentTranscript = Transcript(id, values[0], int(values[3]), int(values[4]), self._getStrand(values[6]), gene_id)
dTranscripts[id] = currentTranscript
if len(dGenes[gene_id].lTranscripts) > 0:
dGenes[gene_id].lTranscripts.append(currentTranscript)
else:
dGenes[gene_id].lTranscripts = [currentTranscript]
if values[2] == 'CDS':
id = self._getFeatureTagValue('ID',values[8])
transcript_id = self._getFeatureTagValue('Parent', values[8])
#id = '{}_CDS'.format(transcript_id)
currentCDS = CDS(id, values[0], int(values[3]), int(values[4]), self._getStrand(values[6]), transcript_id)
if len(dTranscripts[transcript_id].lCDS) > 0:
dTranscripts[transcript_id].lCDS.append(currentCDS)
else:
dTranscripts[transcript_id].lCDS = [currentCDS]
def selectAllGenes(self):
"""Select all genes"""
lGenes = []
dGenes = {}
lTranscripts = []
dTranscripts = {}
lCDS = []
dCDS = {}
cursor = self.conn.execute(
'''select id, seqid, start, end, strand from gene''')
for row in cursor:
dGenes[row[0]] = Gene(row[0], row[1], row[2], row[3], row[4])
cursor = self.conn.execute(
'''select id, seqid, start,end,strand,gene_id from transcript''')
for row in cursor:
transcript = Transcript(row[0], row[1], row[2], row[3], row[4],
row[5])
dTranscripts[row[0]] = transcript
if len(dGenes[transcript.gene_id].lTranscripts) > 0:
dGenes[transcript.gene_id].lTranscripts.append(transcript)
else:
dGenes[transcript.gene_id].lTranscripts = [transcript]
cursor = self.conn.execute(
'''select cds_id, seqid, start,end,strand,transcript_id from cds order by start'''
)
for row in cursor:
cds = CDS(row[0], row[1], row[2], row[3], row[4], row[5])
if len(dTranscripts[cds.transcript_id].lCDS) > 0:
dTranscripts[cds.transcript_id].lCDS.append(cds)
else:
dTranscripts[cds.transcript_id].lCDS = [cds]
return dGenes.values()
def test_getAllGenes(self):
"""Test getAllGenes method"""
iGffGeneParser = GffGeneParser("test-data/gene.gff3")
lGenes = [Gene('G00001','Chr1',23988,24919,-1,[Transcript('G00001.1','Chr1',23988,24919,-1,'G00001',[CDS('G00001.1_cds_1','Chr1',23988,24083, -1, 'G00001.1'),CDS('G00001.1_cds_1','Chr1',24274,24427,-1,'G00001.1'),CDS('G00001.1_cds_1','Chr1',24489,24919,-1,'G00001.1')])])]
self.assertEqual(iGffGeneParser.getAllGenes()[0],lGenes[0])