def read_sam_file(fname):
formatter = SamFormatter()
fp = open(fname)
res = []
for l in fp:
l = l.strip()
if l[0] == "@": # SAM header line
continue
r = formatter.parse(l)
res.append(r)
fp.close()
return res
class SimpleVisitor(object):
def __init__(self):
self.sam = SamFormatter()
self.output = StringIO.StringIO()
def process(self, pair):
for hit in pair:
print >>self.output, self.sam.format(hit)
class EmitSamLink(HitProcessorChainLink):
def __init__(self, context, event_monitor, next_link=None):
super(type(self), self).__init__(next_link)
self.ctx = context
self.output_formatter = SamFormatter(strip_pe_tag=True)
self.event_monitor = event_monitor
def process(self, pair):
for hit in pair:
if hit:
k, v = self.output_formatter.format(hit).split("\t", 1)
self.ctx.emit(str(k), str(v))
self.event_monitor.count("emitted sam records", 1)
super(type(self), self).process(pair) # forward pair to next element in chain
class EmitSamLink(HitProcessorChainLink):
def __init__(self, context, event_monitor, next_link = None):
super(type(self), self).__init__(next_link)
self.ctx = context
self.output_formatter = SamFormatter(strip_pe_tag=True)
self.event_monitor = event_monitor
def process(self, pair):
for hit in pair:
if hit:
k, v = self.output_formatter.format(hit).split("\t", 1)
self.ctx.emit(str(k), str(v))
self.event_monitor.count("emitted sam records", 1)
super(type(self), self).process(pair) # forward pair to next element in chain
def setUp(self):
self.mapping = SimpleMapping()
self.f = SamFormatter()
class TestSamFormatter(unittest.TestCase):
def setUp(self):
self.mapping = SimpleMapping()
self.f = SamFormatter()
def test_default(self):
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_name(self):
self.mapping.set_name("my name")
self.assertEqual("\t".join( map(str, ["my name", 0, "*", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_flag(self):
self.mapping.flag = 163
self.assertEqual("\t".join( map(str, ['', 163, "*", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_reference(self):
self.mapping.tid = "chr21"
self.assertEqual("\t".join( map(str, ['', 0, "chr21", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_mate_reference(self):
self.mapping.mtid = "chr21"
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "chr21", 0, 0, "", "" ])), self.__do_format())
self.mapping.mtid = "="
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "=", 0, 0, "", "" ])), self.__do_format())
def test_pos(self):
self.mapping.pos = 1234
self.assertEqual("\t".join( map(str, ['', 0, "*", 1234, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_mate_pos(self):
self.mapping.mpos = 1234
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 1234, 0, "", "" ])), self.__do_format())
def test_mapq(self):
self.mapping.qual = 55
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 55, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_cigar(self):
self.mapping.set_cigar([ (100, 'M') ])
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "100M", "*", 0, 0, "", "" ])), self.__do_format())
self.mapping.set_cigar([ (80, 'M'), (20, 'S') ])
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "80M20S", "*", 0, 0, "", "" ])), self.__do_format())
def test_isize(self):
self.mapping.isize = 273
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 273, "", "" ])), self.__do_format())
self.mapping.isize = -273
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, -273, "", "" ])), self.__do_format())
def test_seq(self):
self.mapping.set_seq_5("AGCTNN")
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "AGCTNN", "" ])), self.__do_format())
def test_qual(self):
bq = array.array('B', [22, 33, 45])
self.mapping.set_base_qualities(bq)
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "", "7BN" ])), self.__do_format())
def test_tags(self):
self.mapping.add_tag( ("XC", 'i', 18) )
self.mapping.add_tag( ("HI", 'Z', "llo") )
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "", "", "XC:i:18", "HI:Z:llo" ])), self.__do_format())
def __do_format(self):
return self.f.format(self.mapping)
def setUp(self): self.mapping = SimpleMapping() self.f = SamFormatter()
class TestSamFormatter(unittest.TestCase):
def setUp(self):
self.mapping = SimpleMapping()
self.f = SamFormatter()
def test_default(self):
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_name(self):
self.mapping.set_name("my name")
self.assertEqual("\t".join( map(str, ["my name", 0, "*", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_flag(self):
self.mapping.flag = 163
self.assertEqual("\t".join( map(str, ['', 163, "*", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_reference(self):
self.mapping.tid = "chr21"
self.assertEqual("\t".join( map(str, ['', 0, "chr21", 0, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_mate_reference(self):
self.mapping.mtid = "chr21"
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "chr21", 0, 0, "", "" ])), self.__do_format())
self.mapping.mtid = "="
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "=", 0, 0, "", "" ])), self.__do_format())
def test_pos(self):
self.mapping.pos = 1234
self.assertEqual("\t".join( map(str, ['', 0, "*", 1234, 0, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_mate_pos(self):
self.mapping.mpos = 1234
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 1234, 0, "", "" ])), self.__do_format())
def test_mapq(self):
self.mapping.qual = 55
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 55, "*", "*", 0, 0, "", "" ])), self.__do_format())
def test_cigar(self):
self.mapping.set_cigar([ (100, 'M') ])
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "100M", "*", 0, 0, "", "" ])), self.__do_format())
self.mapping.set_cigar([ (80, 'M'), (20, 'S') ])
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "80M20S", "*", 0, 0, "", "" ])), self.__do_format())
def test_isize(self):
self.mapping.isize = 273
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 273, "", "" ])), self.__do_format())
self.mapping.isize = -273
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, -273, "", "" ])), self.__do_format())
def test_seq(self):
self.mapping.set_seq_5("AGCTNN")
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "AGCTNN", "" ])), self.__do_format())
def test_qual(self):
bq = array.array('B', [22, 33, 45])
self.mapping.set_base_qualities(bq)
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "", "7BN" ])), self.__do_format())
def test_tags(self):
self.mapping.add_tag( ("XC", 'i', 18) )
self.mapping.add_tag( ("HI", 'Z', "llo") )
self.assertEqual("\t".join( map(str, ['', 0, "*", 0, 0, "*", "*", 0, 0, "", "", "XC:i:18", "HI:Z:llo" ])), self.__do_format())
def __do_format(self):
return self.f.format(self.mapping)
def __init__(self): self.sam = SamFormatter() self.output = StringIO.StringIO()
def __init__(self, context, event_monitor, next_link=None):
super(EmitSamLink, self).__init__(next_link)
self.ctx = context
self.output_formatter = SamFormatter(strip_pe_tag=True)
self.event_monitor = event_monitor
def __init__(self, context, event_monitor, next_link=None):
super(type(self), self).__init__(next_link)
self.ctx = context
self.output_formatter = SamFormatter(strip_pe_tag=True)
self.event_monitor = event_monitor
def __init__(self):
self.mappings = []
self.formatter = SamFormatter()
