def testSecondExonScheme(self):
"""
check that output exons have the right size and relative indices
from chromosome indices.
"""
# run the code...
infh = DummyInputStream(self.readLines)
outfh = DummyOutputStream()
processBED(infh, outfh, SECOND_EXON)
# see what we get..
outlines = [l.strip() for l in outfh.itemsWritten() if l.strip() != ""]
for i in range(0, len(outlines)):
out = outlines[i]
e2 = parseBEDString(out)
gotAnswer = len(e2)
r_len = self.readEnds[e2.name[:-2]] - self.readStarts[e2.name[:-2]]
glob_s = (self.firstChromStarts[e2.name[:-2]] +
self.readStarts[e2.name[:-2]])
expectedAns = r_len - (self.firstChromEnds[e2.name[:-2]] - (glob_s)) - 1
self.assertTrue(gotAnswer == expectedAns)
self.assertTrue(e2.start == self.secondChromStarts[e2.name[:-2]])
def testFirstExonScheme(self):
"""
check that output exons have the right size and relative indices
from chromosome indices
"""
# run the code...
infh = DummyInputStream(self.readLines)
outfh = DummyOutputStream()
processBED(infh, outfh, FIRST_EXON)
# see what we get..
outlines = [l.strip() for l in outfh.itemsWritten() if l.strip() != ""]
for i in range(0, len(outlines)):
out = outlines[i]
e1 = parseBEDString(out)
gotAnswer = len(e1)
read_start_global = (self.firstChromStarts[e1.name[:-2]] +
self.readStarts[e1.name[:-2]])
expectedAns = self.firstChromEnds[e1.name[:-2]] - read_start_global + 1
self.assertTrue(gotAnswer == expectedAns)
self.assertTrue(e1.end == self.firstChromEnds[e1.name[:-2]])
def testSecondExonScheme(self):
"""
check that output exons have the right size and relative indices
from chromosome indices.
"""
# run the code...
infh = DummyInputStream(self.readLines)
outfh = DummyOutputStream()
processBED(infh, outfh, SECOND_EXON)
# see what we get..
outlines = [l.strip() for l in outfh.itemsWritten() if l.strip() != ""]
for i in range(0, len(outlines)):
out = outlines[i]
e2 = parseBEDString(out)
gotAnswer = len(e2)
r_len = self.readEnds[e2.name[:-2]] - self.readStarts[e2.name[:-2]]
glob_s = (self.firstChromStarts[e2.name[:-2]] +
self.readStarts[e2.name[:-2]])
expectedAns = r_len - (self.firstChromEnds[e2.name[:-2]] -
(glob_s)) - 1
self.assertTrue(gotAnswer == expectedAns)
self.assertTrue(e2.start == self.secondChromStarts[e2.name[:-2]])
def testFirstExonScheme(self):
"""
check that output exons have the right size and relative indices
from chromosome indices
"""
# run the code...
infh = DummyInputStream(self.readLines)
outfh = DummyOutputStream()
processBED(infh, outfh, FIRST_EXON)
# see what we get..
outlines = [l.strip() for l in outfh.itemsWritten() if l.strip() != ""]
for i in range(0, len(outlines)):
out = outlines[i]
e1 = parseBEDString(out)
gotAnswer = len(e1)
read_start_global = (self.firstChromStarts[e1.name[:-2]] +
self.readStarts[e1.name[:-2]])
expectedAns = self.firstChromEnds[
e1.name[:-2]] - read_start_global + 1
self.assertTrue(gotAnswer == expectedAns)
self.assertTrue(e1.end == self.firstChromEnds[e1.name[:-2]])
def testBEDIteratorDropAfter(self):
"""
make sure we can drop parts after a certain field in a BED file and
not screw everything else up..
"""
debug = False
infs = "chr12" + "\t" + "83810028" + "\t" + "83810066" + "\t" +\
"SRR189775.10000" + "\t" + "9" + "\t" + "-" + "\t" +\
"TTTTTTTTTTTTTTTAAATTCTTCGAATGCCGTTTTCT" + "\t" +\
"]&(2-'+0'+:34J########################\n" +\
"chr5" + "\t" + "177570573" + "\t" + "177570611" + "\t" +\
"SRR189775.10000001" + "\t" + "3" + "\t" + "+" + "\t" +\
"TCACCTTTTTTTCACCTTTTAATTTTATATTATTTATC" + "\t" +\
"K79:77:79797:7797<;>BC979:77B?997:79:7\n" +\
"chr4" + "\t" + "78174772" + "\t" + "78174810" + "\t" +\
"SRR189775.10000009" + "\t" + "0" + "\t" + "+" + "\t" +\
"TTTTATTTTATTTTATTTTTTTACCCTTCCTCAAACAC" + "\t" +\
"G77:797:77977<TS;:9:9:9:9:977<;7@?@=97\n"
expectOut = [
"chr12" + "\t" + "83810028" + "\t" + "83810066" + "\t"
"SRR189775.10000" + "\t" + "9" + "\t" + "-",
"chr5" + "\t" + "177570573" + "\t" + "177570611" + "\t" +
"SRR189775.10000001" + "\t" + "3" + "\t" + "+",
"chr4" + "\t" + "78174772" + "\t" + "78174810" + "\t" +
"SRR189775.10000009" + "\t" + "0" + "\t" + "+"
]
ifh = DummyInputStream(infs)
ofh = DummyOutputStream()
def run(istrm, ostrm):
for e in BEDIterator(istrm, dropAfter=6):
ostrm.write(str(e) + "\n")
run(ifh, ofh)
gotOutput = [x.strip() for x in ofh.itemsWritten()]
if debug:
sys.stderr.write("expected -------\n")
for e in expectOut:
sys.stderr.write(e + "\n")
sys.stderr.write("got ------------\n")
for e in gotOutput:
sys.stderr.write(e + "\n")
self.assertTrue(gotOutput == expectOut)
def testSimpleKeys(self):
debug = False
infh = DummyInputStream(self.exonCounts)
inref = DummyInputStream(self.genes)
outfh = DummyOutputStream()
process(infh, inref, outfh, verbose=False, debug=debug)
gotOutput = outfh.itemsWritten()
if debug:
print "expected -------"
for e in self.expectedAns:
print e
print "got ------------"
for e in gotOutput:
print e
assert(self.expectedAns == gotOutput)
def testBEDIteratorDropAfter(self):
"""
make sure we can drop parts after a certain field in a BED file and
not screw everything else up..
"""
debug = False
infs = "chr12" + "\t" + "83810028" + "\t" + "83810066" + "\t" +\
"SRR189775.10000" + "\t" + "9" + "\t" + "-" + "\t" +\
"TTTTTTTTTTTTTTTAAATTCTTCGAATGCCGTTTTCT" + "\t" +\
"]&(2-'+0'+:34J########################\n" +\
"chr5" + "\t" + "177570573" + "\t" + "177570611" + "\t" +\
"SRR189775.10000001" + "\t" + "3" + "\t" + "+" + "\t" +\
"TCACCTTTTTTTCACCTTTTAATTTTATATTATTTATC" + "\t" +\
"K79:77:79797:7797<;>BC979:77B?997:79:7\n" +\
"chr4" + "\t" + "78174772" + "\t" + "78174810" + "\t" +\
"SRR189775.10000009" + "\t" + "0" + "\t" + "+" + "\t" +\
"TTTTATTTTATTTTATTTTTTTACCCTTCCTCAAACAC" + "\t" +\
"G77:797:77977<TS;:9:9:9:9:977<;7@?@=97\n"
expectOut = ["chr12" + "\t" + "83810028" + "\t" + "83810066" + "\t"
"SRR189775.10000" + "\t" + "9" + "\t" + "-",
"chr5" + "\t" + "177570573" + "\t" + "177570611" + "\t" +
"SRR189775.10000001" + "\t" + "3" + "\t" + "+",
"chr4" + "\t" + "78174772" + "\t" + "78174810" + "\t" +
"SRR189775.10000009" + "\t" + "0" + "\t" + "+"]
ifh = DummyInputStream(infs)
ofh = DummyOutputStream()
def run(istrm, ostrm):
for e in BEDIterator(istrm, dropAfter=6):
ostrm.write(str(e) + "\n")
run(ifh, ofh)
gotOutput = [x.strip() for x in ofh.itemsWritten()]
if debug:
sys.stderr.write("expected -------\n")
for e in expectOut:
sys.stderr.write(e + "\n")
sys.stderr.write("got ------------\n")
for e in gotOutput:
sys.stderr.write(e + "\n")
self.assertTrue(gotOutput == expectOut)
