def test_no_context(self):
genome = Genome(self.gdfilepath)
chr1 = genome["chr1"]
tracknames = genome.tracknames_continuous
data = chr1[100:1000] # Used to segfault
chr2 = genome["chrY"]
chr2.close() # Make sure manual close doesn't break it
self.assertTrue(chr1.isopen)
self.assertFalse(chr2.isopen)
genome.close()
self.assertFalse(chr1.isopen)
self.assertRaises(Exception, iter(chr1).next)
def test_no_context(self):
genome = Genome(self.gdfilepath)
chr1 = genome["chr1"]
genome.tracknames_continuous # test access
chr1[100:1000] # test access: at one point segfaulted
chr2 = genome["chrY"]
chr2.close() # Make sure manual close doesn't break it
self.assertTrue(chr1.isopen)
self.assertFalse(chr2.isopen)
genome.close()
self.assertFalse(chr1.isopen)
self.assertRaises(Exception, next, iter(chr1))
def test_repr_str(self):
genome = Genome(self.gdfilepath, mode="r")
self.assertEqual(repr(genome),
"Genome('%s', **{'mode': 'r'})" % self.gdfilepath)
chr = genome["chr1"]
if self.mode == "dir":
self.assertEqual(
repr(chr), "<Chromosome 'chr1', file='%s/chr1.genomedata'>" %
self.gdfilepath)
self.assertEqual(str(chr), "chr1")
elif self.mode == "file":
self.assertEqual(
repr(chr), "<Chromosome 'chr1', file='%s'>" % self.gdfilepath)
self.assertEqual(str(chr), "chr1")
genome.close()
def test_repr_str(self):
genome = Genome(self.gdfilepath, mode="r")
self.assertEqual(repr(genome), "Genome('%s', **{'mode': 'r'})" %
self.gdfilepath)
chr = genome["chr1"]
if self.mode == "dir":
self.assertEqual(repr(chr),
"<Chromosome 'chr1', file='%s/chr1.genomedata'>" %
self.gdfilepath)
self.assertEqual(str(chr), "chr1")
elif self.mode == "file":
self.assertEqual(repr(chr),
"<Chromosome 'chr1', file='%s'>" %
self.gdfilepath)
self.assertEqual(str(chr), "chr1")
genome.close()
INFO = True
outFile.writelines(line)
else:
# rest of the VCF file should now just be the variants
if line == "":
break
line = line.decode('utf-8').strip().split('\t')
if line[0] != currentChrom:
chrom = genome["chr"+line[0]]
currentChrom = "chr"+line[0]
pos = int(line[1]) - 1 #switch to zero based indexing
score = chrom[pos,'anc']
# check to see if there is a GERP score for the position, if not output line and continue
# We should probably check ot see if the variant is not a SNP, as GERP isn't well defined
# for non-SNP variants
if math.isnan(score):
anc = '.'
else:
anc = chr(score)
if line[7] == '.':
line[7] = 'AA=%s' % (anc.upper())
else :
rsField = ';AA=%s' % (anc.upper())
line[7] += rsField
outFile.writelines('\t'.join(line)+'\n')
genome.close()
inFile.close()
outFile.close()
