def testChrom2HashCodeTable(self):
chroms = ["1", "X", "3", "contig1", "Y", "25", "mt"]
h = MutUtils.createChrom2HashCodeTable(chroms)
self.assertTrue(
h["1"] == 1,
"For chrom 1, hash code should be 1 but it was %s." % h["1"])
self.assertTrue(
h["3"] == 3,
"For chrom 3, hash code should be 3 but it was %s." % h["3"])
self.assertTrue(
h["25"] == 25,
"For chrom 25, hash code should be 25 but it was %s." % h["25"])
self.assertTrue(
h["X"] == 26,
"For chrom X, hash code should be 26 but it was %s." % h["X"])
self.assertTrue(
h["Y"] == 27,
"For chrom Y, hash code should be 27 but it was %s." % h["Y"])
self.assertTrue(
h["mt"] == 28,
"For chrom mt, hash code should be 28 but it was %s." % h["mt"])
self.assertTrue(
h["contig1"] == 29,
"For chrom contig1, hash code should be 29 but it was %s." %
h["contig1"])
chroms = ["contig1", "mt"]
h = MutUtils.createChrom2HashCodeTable(chroms)
self.assertTrue(
h["mt"] == 3,
"For chrom mt, hash code should be 3 but it was %s." % h["mt"])
self.assertTrue(
h["contig1"] == 4,
"For chrom contig1, hash code should be 4 but it was %s." %
h["contig1"])
def testChrom2HashCodeTable(self):
chroms = ["1", "X", "3", "contig1", "Y", "25", "mt"]
h = MutUtils.createChrom2HashCodeTable(chroms)
self.assertTrue(h["1"] == 1, "For chrom 1, hash code should be 1 but it was %s." % h["1"])
self.assertTrue(h["3"] == 3, "For chrom 3, hash code should be 3 but it was %s." % h["3"])
self.assertTrue(h["25"] == 25, "For chrom 25, hash code should be 25 but it was %s." % h["25"])
self.assertTrue(h["X"] == 26, "For chrom X, hash code should be 26 but it was %s." % h["X"])
self.assertTrue(h["Y"] == 27, "For chrom Y, hash code should be 27 but it was %s." % h["Y"])
self.assertTrue(h["mt"] == 28, "For chrom mt, hash code should be 28 but it was %s." % h["mt"])
self.assertTrue(h["contig1"] == 29, "For chrom contig1, hash code should be 29 but it was %s." % h["contig1"])
chroms = ["contig1", "mt"]
h = MutUtils.createChrom2HashCodeTable(chroms)
self.assertTrue(h["mt"] == 3, "For chrom mt, hash code should be 3 but it was %s." % h["mt"])
self.assertTrue(h["contig1"] == 4, "For chrom contig1, hash code should be 4 but it was %s." % h["contig1"])
def getSortedTsvFilename(self, path):
"""
:param path:
:return:
"""
chrom2HashCode = MutUtils.createChrom2HashCodeTable(self.chroms)
tsvFileSorter = TsvFileSorter(self.filename)
sortedTempTsvFile = tempfile.NamedTemporaryFile(dir=path, delete=False)
func = lambda val: (chrom2HashCode[val["chr"]], int(val["start"]), val["alt_allele"])
tsvFileSorter.sortFile(sortedTempTsvFile.name, func)
os.remove(self.filename)
return sortedTempTsvFile.name
def getSortedTsvFilename(self, path):
"""
:param path:
:return:
"""
chrom2HashCode = MutUtils.createChrom2HashCodeTable(self.chroms)
tsvFileSorter = TsvFileSorter(self.filename)
sortedTempTsvFile = tempfile.NamedTemporaryFile(dir=path, delete=False)
func = lambda val: (chrom2HashCode[val["chr"]], int(val["start"]), val["alt_allele"])
self.logger.debug("Sorting tmp tsv %s->%s", self.filename, sortedTempTsvFile.name)
tsvFileSorter.sortFile(sortedTempTsvFile.name, func)
os.remove(self.filename)
return sortedTempTsvFile.name
