def run(acc, splitNum, splitNo):
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(acc) as run:
run_name = run.getName()
# compute window to iterate through
MAX_ROW = run.getReadCount()
chunk = MAX_ROW / splitNum
first = int(round(chunk * (splitNo - 1)))
next_first = int(round(chunk * (splitNo)))
if next_first > MAX_ROW:
next_first = MAX_ROW
# start iterator on reads
with run.getReadRange(first + 1, next_first - first, Read.all) as it:
i = 0
while it.nextRead():
i += 1
print(it.getReadId())
# iterate through fragments
while it.nextFragment():
bases = it.getFragmentBases()
if bases:
print("\t{} - {}".format(
bases,
"aligned" if it.isAligned() else "unaligned"))
print("\n")
print("Read {} spots for {}".format(i, run_name))
def run(acc, splitNum, splitNo):
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(acc) as run:
run_name = run.getName()
# compute window to iterate through
MAX_ROW = run.getReadCount()
chunk = MAX_ROW/splitNum
first = int(round(chunk*(splitNo-1)))
next_first = int(round(chunk*(splitNo)))
if next_first > MAX_ROW:
next_first = MAX_ROW
# start iterator on reads
with run.getReadRange(first+1, next_first-first, Read.all) as it:
i = 0
while it.nextRead():
i += 1
print (it.getReadId())
# iterate through fragments
while it.nextFragment():
bases = it.getFragmentBases()
if bases:
print ("\t{} - {}".format(bases, "aligned" if it.isAligned() else "unaligned"))
print ("\n")
print ("Read {} spots for {}".format(i, run_name))
def run(acc, splitNum, splitNo):
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(acc) as run:
run_name = run.getName()
# compute window to iterate through
MAX_ROW = run.getAlignmentCount()
chunk = MAX_ROW / splitNum
first = int(round(chunk * (splitNo-1)))
next_first = int(round(chunk * (splitNo)))
if next_first > MAX_ROW:
next_first = MAX_ROW
# start iterator on reads
with run.getAlignmentRange(first+1, next_first-first, Alignment.primaryAlignment) as it:
i = 0
while it.nextAlignment():
print ("{}\t{}\t{}\t{}\t{}\t{}".format(it.getReadId(),
it.getReferenceSpec(),
it.getAlignmentPosition(),
it.getShortCigar(False),
it.getFragmentBases(),
("aligned" if it.isAligned() else "unaligned"),
))
i += 1
print ("Read {} alignments for {}".format(i, run_name))
def sra_reader(accn, batch_size=1000, max_reads=None):
"""Iterates through a read collection for a given accession number using
the ngs-lib python bindings.
Args:
accn: The accession number
batch_size: The maximum number of reads to request in each call to SRA
max_reads: The total number of reads to process, or all reads in the
SRA run if None
Yields:
Each pair of reads (see ``sra_read_pair``)
"""
with NGS.openReadCollection(accn) as run:
run_name = run.getName()
read_count = run.getReadCount()
if max_reads:
max_reads = min(read_count, max_reads)
else:
max_reads = read_count
for batch_num, first_read in enumerate(range(1, max_reads,
batch_size)):
cur_batch_size = min(batch_size, max_reads - first_read + 1)
with run.getReadRange(first_read, cur_batch_size,
Read.all) as read:
for read_idx in range(cur_batch_size):
read.nextRead()
yield sra_read_pair(read)
def test_ReadGroupIterator_ThrowBeforeNext(self):
it = NGS.openReadCollection(PrimaryOnly).getReadGroups()
try:
it.getName()
self.fail()
except ErrorMsg:
pass
def run(acc, splitNum, splitNo): # this function doesn't release NGS objects however it might
# open requested accession using SRA implementation of the API
run = NGS.openReadCollection(acc)
run_name = run.getName()
# compute window to iterate through
MAX_ROW = run.getReadCount()
chunk = MAX_ROW/splitNum
first = int(round(chunk*(splitNo-1)))
next_first = int(round(chunk*(splitNo)))
if next_first > MAX_ROW:
next_first = MAX_ROW
# start iterator on reads
it = run.getReadRange(first+1, next_first-first, Read.all)
i = 0
while it.nextRead():
i += 1
print (it.getReadId())
# iterate through fragments
while it.nextFragment():
bases = it.getFragmentBases()
if bases:
print ("\t" + bases + " - " + ("aligned" if it.isAligned() else "unaligned"))
print ("\n")
print ("Read {} spots for {}".format(i, run_name))
def run(acc, splitNum, splitNo): # this function doesn't release NGS objects however it might
# open requested accession using SRA implementation of the API
run = NGS.openReadCollection(acc)
run_name = run.getName()
# compute window to iterate through
MAX_ROW = run.getAlignmentCount()
chunk = MAX_ROW / splitNum
first = int(round(chunk * (splitNo - 1)))
next_first = int(round(chunk * (splitNo)))
if next_first > MAX_ROW:
next_first = MAX_ROW
# start iterator on reads
it = run.getAlignmentRange(first + 1, next_first - first, Alignment.primaryAlignment)
i = 0
while it.nextAlignment():
print(
it.getReadId()
+ "\t"
+ it.getReferenceSpec()
+ "\t"
+ str(it.getAlignmentPosition())
+ "\t"
+ it.getShortCigar(False)
+ "\t"
+ it.getFragmentBases()
+ "\t"
+ ("aligned" if it.isAligned() else "unaligned")
)
i += 1
print("Read {} alignments for {}".format(i, run_name))
def run(acc, splitNum,
splitNo): # this function doesn't release NGS objects however it might
# open requested accession using SRA implementation of the API
run = NGS.openReadCollection(acc)
run_name = run.getName()
# compute window to iterate through
MAX_ROW = run.getReadCount()
chunk = MAX_ROW / splitNum
first = int(round(chunk * (splitNo - 1)))
next_first = int(round(chunk * (splitNo)))
if next_first > MAX_ROW:
next_first = MAX_ROW
# start iterator on reads
it = run.getReadRange(first + 1, next_first - first, Read.all)
i = 0
while it.nextRead():
i += 1
print(it.getReadId())
# iterate through fragments
while it.nextFragment():
bases = it.getFragmentBases()
if bases:
print("\t" + bases + " - " +
("aligned" if it.isAligned() else "unaligned"))
print("\n")
print("Read {} spots for {}".format(i, run_name))
def run(acc, splitNum, splitNo): # this function doesn't release NGS objects however it might
# open requested accession using SRA implementation of the API
run = NGS.openReadCollection(acc)
run_name = run.getName()
# compute window to iterate through
MAX_ROW = run.getAlignmentCount()
chunk = MAX_ROW / splitNum
first = int(round(chunk * (splitNo-1)))
next_first = int(round(chunk * (splitNo)))
if next_first > MAX_ROW:
next_first = MAX_ROW
# start iterator on reads
it = run.getAlignmentRange(first+1, next_first-first, Alignment.primaryAlignment)
i = 0
while it.nextAlignment():
print (
it.getReadId() + "\t" +
it.getReferenceSpec() + "\t" +
str(it.getAlignmentPosition()) + "\t" +
it.getShortCigar(False) + "\t" +
it.getFragmentBases()
)
i += 1
print ("Read {} alignments for {}".format(i, run_name))
def stream_reads(self, acc, event, splitNum=1, splitNo=1):
'''
This is a blocking task, it needs to be run in an executor
'''
# open requested accession using SRA implementation of the API
print(f'Streaming {acc}', file=sys.stderr)
pipe_path = self.get_pipe(acc)
pipe = open(pipe_path, 'w')
event.clear()
with NGS.openReadCollection(acc) as run:
run_name = run.getName()
# compute window to iterate through
MAX_ROW = run.getReadCount()
chunk = MAX_ROW/splitNum
first = int(round(chunk*(splitNo-1)))
next_first = int(round(chunk*(splitNo)))
if next_first > MAX_ROW:
next_first = MAX_ROW
# start iterator on reads
with run.getReadRange(first+1, next_first-first, Read.all) as it:
i = 0
while it.nextRead():
i += 1
if i > 20000:
break
while it.nextFragment():
bases = it.getFragmentBases()
qualities=it.getFragmentQualities()
ids=it.getFragmentId()
if bases:
read = f'@{ids}\n{bases}\n+\n{qualities}'
print(read,file=pipe)
os.unlink(pipe_path)
print(f'Done streaming for {acc}')
return None
def run(acc, splitNum, splitNo):
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(acc) as run:
run_name = run.getName()
# compute window to iterate through
MAX_ROW = run.getAlignmentCount()
chunk = MAX_ROW / splitNum
first = int(round(chunk * (splitNo - 1)))
next_first = int(round(chunk * (splitNo)))
if next_first > MAX_ROW:
next_first = MAX_ROW
# start iterator on reads
with run.getAlignmentRange(first + 1, next_first - first,
Alignment.primaryAlignment) as it:
i = 0
while it.nextAlignment():
print("{}\t{}\t{}\t{}\t{}".format(
it.getReadId(),
it.getReferenceSpec(),
it.getAlignmentPosition(),
it.getShortCigar(False),
it.getFragmentBases(),
))
i += 1
print("Read {} alignments for {}".format(i, run_name))
def run(acc, refName, start, stop):
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(acc) as run:
run_name = run.getName()
# get requested reference
with run.getReference(refName) as ref:
# start iterator on requested range
with ref.getPileupSlice(start - 1, stop - start + 1) as it:
i = 0
while it.nextPileup():
qual = ""
base = ""
line = "{}\t{}\t{}\t{}".format(
it.getReferenceSpec(), it.getReferencePosition() + 1, it.getReferenceBase(), it.getPileupDepth()
)
while it.nextPileupEvent():
e = it.getEventType()
if (e & PileupEvent.alignment_start) != 0:
base = base + "^"
base = base + chr(it.getMappingQuality() + 33)
if (e & PileupEvent.insertion) != 0:
base = base + "+"
ibases = it.getInsertionBases()
c = len(ibases)
base = base + str(c)
if (e & PileupEvent.alignment_minus_strand) != 0:
base = base + ibases.lower()
else:
base = base + ibases
evt = e & 7
if (e & PileupEvent.alignment_minus_strand) != 0:
if evt == PileupEvent.deletion:
base = base + "<"
elif evt == PileupEvent.match:
base = base + ","
elif evt == PileupEvent.mismatch:
base = base + str(it.getAlignmentBase()).lower()
else:
if evt == PileupEvent.deletion:
base = base + ">"
elif evt == PileupEvent.match:
base = base + "."
elif evt == PileupEvent.mismatch:
base = base + str(it.getAlignmentBase()).upper()
if (e & PileupEvent.alignment_stop) != 0:
base = base + "$"
qual = qual + it.getAlignmentQuality()
i += 1
print("{}\t{}\t{}".format(line, base, qual))
print("Read {} pileups for {}".format(i, run_name))
def test_ReferenceWindow_Slice_Filtered_Category (self):
it = NGS.openReadCollection(WithSecondary).getReference("gi|169794206|ref|NC_010410.1|").getAlignmentSlice(516000, 100000, Alignment.primaryAlignment)
self.assertTrue(it.nextAlignment())
self.assertEqual(WithSecondary + ".PA.33", it. getAlignmentId())
self.assertTrue(it.nextAlignment())
self.assertEqual(WithSecondary + ".PA.34", it. getAlignmentId())
self.assertTrue(it.nextAlignment())
self.assertEqual(WithSecondary + ".PA.35", it. getAlignmentId()) # no secondary
self.assertFalse(it.nextAlignment())
def search_reads(request):
""" Searches a genomic interval in the NCBI API and returns a list of converted GA4GH alignments
Args:
request: SearchReadsRequest. If `request.page_size` is set, up to this many records are returned.
If not set, `_DEFAULT_PAGE_SIZE` is used as the page size.
`request.start` can be overridden by providing a greater start position in `request.page_token`.
If provided, `request.page_token` is parsed to a long and compared with `request.start`.
In that case, the greater of the two is used as the zero-based inclusive interval start.
Returns:
Tuple:
1) List of converted alignments in GA4GH schema
2) Maximum zero-based exclusive alignment end position over all alignments returned.
This value can be set as request.page_token (after parsing to a string) for a subsequent
request; in that case, streaming will pick up where it left off after this request.
"""
# We are assuming the read group IDs are singleton
run_accession = request.read_group_ids[0]
reference_name = request.reference_id
# Choose the start position between request.start and request.page_token
try:
start = max(long(request.page_token), request.start)
except ValueError:
start = request.start
end = request.end
# Number of alignments to get
if request.page_size < 1:
num_aligns = _DEFAULT_PAGE_SIZE
else:
num_aligns = request.page_size
alignments = []
max_aligned_pos = 0 # Keep track of max zero-based exclusive alignment end
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(run_accession) as run:
# get requested reference
with run.getReference(reference_name) as reference:
# start iterator on requested range
# We need to find out if it returns overlapping reads, or just
# those that fit within the slice.
with reference.getAlignmentSlice(start, end - start + 1,
Alignment.primaryAlignment) as it:
i = 0
while it.nextAlignment():
# Only get the requested number of alignments
if i == num_aligns:
break
max_aligned_pos = max(
max_aligned_pos,
it.getAlignmentPosition() + it.getAlignmentLength())
ga_alignment = _convert_alignment(it)
alignments.append(ga_alignment)
i += 1
return (alignments, max_aligned_pos)
def test_ReadGroup_getStatistics(self):
gr = NGS.openReadCollection(WithGroups).getReadGroup("GS57510-FS3-L03")
stats = gr.getStatistics()
self.assertEqual(34164461870, stats.getAsU64("BASE_COUNT"))
self.assertEqual(34164461870, stats.getAsU64("BIO_BASE_COUNT"))
self.assertEqual(488063741, stats.getAsU64("SPOT_COUNT"))
self.assertEqual(5368875807, stats.getAsU64("SPOT_MAX"))
self.assertEqual(4880812067, stats.getAsU64("SPOT_MIN"))
def test_ReferenceWindow_Slice_Filtered_Start_Within_Slice (self):
ref = NGS.openReadCollection(WithCircularRef).getReference("NC_012920.1")
it = ref.getFilteredAlignmentSlice(0, ref.getLength(), Alignment.all, Alignment.startWithinSlice, 0)
self.assertTrue(it.nextAlignment())
lastAlignmentPosition = it.getAlignmentPosition()
while it.nextAlignment():
currentPosition = it.getAlignmentPosition()
errorMsg = "Sorting violated. Last position (" + str(lastAlignmentPosition) + ") is higher than current one (" + str(currentPosition) + ")"
self.assertTrue ( lastAlignmentPosition <= currentPosition, errorMsg )
lastAlignmentPosition = currentPosition
def test_Alignment_isPaired_MultiFragmentsPerSpot(self):
readCollection = NGS.openReadCollection(PrimaryOnly)
alignment = readCollection.getAlignment(PrimaryOnly + ".PA.1")
self.assertTrue(alignment.isPaired())
alignment = readCollection.getAlignment(PrimaryOnly + ".PA.2")
self.assertTrue(alignment.isPaired())
# has unaligned mate
alignment = readCollection.getAlignment (PrimaryOnly + ".PA.6")
self.assertTrue(alignment.isPaired())
def run(acc, refName=None):
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(acc) as run:
if refName:
with run.getReference(refName) as ref:
process(ref)
else:
with run.getReferences() as refs:
while refs.nextReference():
process(refs)
print("")
def run(acc, refName=None):
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(acc) as run:
if refName:
with run.getReference(refName) as ref:
process(ref)
else:
with run.getReferences() as refs:
while refs.nextReference():
process(refs)
print("")
def start(self):
"""Open the read collection.
"""
self.read_collection = NGS.openReadCollection(self.accn)
self.run_name = self.read_collection.getName()
self.read_count = self.read_collection.getReadCount()
# grab the first read use it to determine whether the dataset
# is single- or paired-end
with self.read_collection.getReadRange(1, 1, Read.all) as read:
read.nextRead()
self.frag_count = len(sra_reads(read))
def run(acc): # this function doesn't release NGS objects however it might
# open requested accession using SRA implementation of the API
run = NGS.openReadCollection(acc)
run_name = run.getName()
# get requested reference
it = run.getReferences()
i = 0
while it.nextReference():
print(it.getCommonName() + "\t" + it.getCanonicalName() + "\t" +
str(it.getLength()) + "\t" +
("circular" if it.getIsCircular() else "linear"))
print("Read {} references for {}".format(i, run_name))
def main():
parser = argparse.ArgumentParser(description='produce FastQ using NGS')
parser.add_argument('accession',
default=None,
type=str,
help='accession to process')
parser.add_argument('-s',
'--start',
default=1,
type=int,
help='first row to use')
parser.add_argument('-n',
'--count',
default=10,
type=int,
help='number of rows to use')
parser.add_argument('-p',
'--split',
default=False,
action='store_true',
help='split the READS')
parser.add_argument('-r',
'--random',
default=False,
action='store_true',
help='get n random rows')
args = parser.parse_args()
if args.accession == None:
print("accession missing!")
else:
try:
with NGS.openReadCollection(args.accession) as run:
if args.random:
if args.split:
src = random_fastq_split(run, args.count)
else:
src = random_fastq(run, args.count)
else:
if args.split:
src = fastq_split(run, args.start, args.count)
else:
src = fastq(run, args.start, args.count)
for read in src:
printfastq(*read)
except ErrorMsg as e:
print("error: {}".format(e))
def run(acc):
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(acc) as run:
run_name = run.getName()
# get requested reference
with run.getReferences() as it:
i = 0
while it.nextReference():
print ("{}\t{}\t{}\t{}".format(it.getCommonName(),
it.getCanonicalName(),
it.getLength(),
"circular" if it.getIsCircular() else "linear",
))
print ("Read {} references for {}".format(i, run_name))
def run(acc):
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(acc) as run:
run_name = run.getName()
# get requested reference
with run.getReferences() as it:
i = 0
while it.nextReference():
print("{}\t{}\t{}\t{}".format(
it.getCommonName(),
it.getCanonicalName(),
it.getLength(),
"circular" if it.getIsCircular() else "linear",
))
print("Read {} references for {}".format(i, run_name))
def run(acc): # this function doesn't release NGS objects however it might
# open requested accession using SRA implementation of the API
run = NGS.openReadCollection(acc)
run_name = run.getName()
# get requested reference
it = run.getReferences()
i = 0
while it.nextReference():
print (
it.getCommonName() + "\t" +
it.getCanonicalName() + "\t" +
str(it.getLength()) + "\t" +
("circular" if it.getIsCircular() else "linear")
)
print ("Read {} references for {}".format(i, run_name))
def test_ReferenceWindow(self):
it = NGS.openReadCollection(WithSecondary).getReference("gi|169794206|ref|NC_010410.1|").getAlignments(Alignment.all)
self.assertTrue(it.nextAlignment())
# the first 2 secondary alignments' locations on the list: #34, #61
count = 1;
while it.nextAlignment():
if it.getAlignmentCategory() == Alignment.secondaryAlignment:
break
count += 1
self.assertEqual(34, count)
while it.nextAlignment():
if it.getAlignmentCategory() == Alignment.secondaryAlignment:
break
count += 1
self.assertEqual(61, count)
def run(acc, refName, start, stop):
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(acc) as run:
run_name = run.getName()
# get requested reference
with run.getReference(refName) as ref:
# start iterator on requested range
with ref.getAlignmentSlice(start, stop-start+1, Alignment.primaryAlignment) as it:
i = 0
while it.nextAlignment():
print ("{}\t{}\t{}\t{}\t{}".format(
it.getReadId(),
it.getReferenceSpec(),
it.getAlignmentPosition(),
it.getLongCigar(False),
it.getAlignedFragmentBases(),
))
i += 1
print ("Read {} alignments for {}".format(i, run_name))
def run(acc, refName, start, stop):
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(acc) as run:
run_name = run.getName()
# get requested reference
with run.getReference(refName) as ref:
# start iterator on requested range
with ref.getAlignmentSlice(start, stop-start+1, Alignment.primaryAlignment) as it:
i = 0
while it.nextAlignment():
print ("{}\t{}\t{}\t{}\t{}".format(
it.getReadId(),
it.getReferenceSpec(),
it.getAlignmentPosition(),
it.getLongCigar(False),
it.getAlignedFragmentBases(),
))
i += 1
print ("Read {} alignments for {}".format(i, run_name))
def run(acc, refName, start, stop): # this function doesn't release NGS objects however it might
# open requested accession using SRA implementation of the API
run = NGS.openReadCollection(acc)
run_name = run.getName()
# get requested reference
ref = run.getReference(refName)
# start iterator on requested range
it = ref.getAlignmentSlice(start, stop-start+1, Alignment.primaryAlignment)
i = 0
while it.nextAlignment():
print ("%s\t%s\t%d\t%s\t%s" % (
it.getReadId(),
it.getReferenceSpec(),
it.getAlignmentPosition(),
it.getLongCigar(False),
it.getAlignedFragmentBases(),
))
i += 1
print ("Read %d alignments for %s" % (i, run_name))
def sra_reader(accn, batcher):
"""Iterates through a read collection for a given accession number using
the ngs-lib python bindings.
Args:
accn: The accession number
batch_size: The maximum number of reads to request in each call to SRA
max_reads: The total number of reads to process, or all reads in the
SRA run if None
Yields:
Each pair of reads (see ``sra_read_pair``)
"""
with NGS.openReadCollection(accn) as run:
run_name = run.getName()
read_count = run.getReadCount()
for batch, start, size in batcher(read_count):
with run.getReadRange(start + 1, size, Read.all) as read:
for read_idx in range(size):
read.nextRead()
yield sra_read(read)
def run(acc, refName, start,
stop): # this function doesn't release NGS objects however it might
# open requested accession using SRA implementation of the API
run = NGS.openReadCollection(acc)
run_name = run.getName()
# get requested reference
ref = run.getReference(refName)
# start iterator on requested range
it = ref.getAlignmentSlice(start, stop - start + 1,
Alignment.primaryAlignment)
i = 0
while it.nextAlignment():
print("%s\t%s\t%d\t%s\t%s" % (
it.getReadId(),
it.getReferenceSpec(),
it.getAlignmentPosition(),
it.getLongCigar(False),
it.getAlignedFragmentBases(),
))
i += 1
print("Read %d alignments for %s" % (i, run_name))
def test_ReadCollection_getName(self):
self.assertEqual(PrimaryOnly, NGS.openReadCollection(PrimaryOnly).getName())
def test_ReadGroupIterator_Next(self):
it = NGS.openReadCollection(PrimaryOnly).getReadGroups();
self.assertTrue(it.nextReadGroup());
name = it.getName();
def test_ReadCollection_getReadGroups(self):
it = NGS.openReadCollection(PrimaryOnly).getReadGroups()
def test_ReadCollection_getReadGroup(self):
gr = NGS.openReadCollection(PrimaryOnly).getReadGroup("C1ELY.6")
def test_ReadCollection_getReferences(self):
it = NGS.openReadCollection(PrimaryOnly).getReferences()
def run(acc, refName, start, stop):
# open requested accession using SRA implementation of the API
with NGS.openReadCollection(acc) as run:
run_name = run.getName()
# get requested reference
with run.getReference(refName) as ref:
# start iterator on requested range
with ref.getPileupSlice(start - 1, stop - start + 1) as it:
i = 0
while it.nextPileup():
qual = ""
base = ""
line = "{}\t{}\t{}\t{}".format(
it.getReferenceSpec(),
it.getReferencePosition() + 1,
it.getReferenceBase(),
it.getPileupDepth(),
)
while it.nextPileupEvent():
e = it.getEventType()
if (e & PileupEvent.alignment_start) != 0:
base = base + '^'
base = base + chr(it.getMappingQuality() + 33)
if (e & PileupEvent.insertion) != 0:
base = base + '+'
ibases = it.getInsertionBases()
c = len(ibases)
base = base + str(c)
if (e & PileupEvent.alignment_minus_strand) != 0:
base = base + ibases.lower()
else:
base = base + ibases
evt = e & 7
if (e & PileupEvent.alignment_minus_strand) != 0:
if evt == PileupEvent.deletion:
base = base + '<'
elif evt == PileupEvent.match:
base = base + ','
elif evt == PileupEvent.mismatch:
base = base + str(
it.getAlignmentBase()).lower()
else:
if evt == PileupEvent.deletion:
base = base + '>'
elif evt == PileupEvent.match:
base = base + '.'
elif evt == PileupEvent.mismatch:
base = base + str(
it.getAlignmentBase()).upper()
if (e & PileupEvent.alignment_stop) != 0:
base = base + '$'
qual = qual + it.getAlignmentQuality()
i += 1
print("{}\t{}\t{}".format(line, base, qual))
print("Read {} pileups for {}".format(i, run_name))
def test_ReadCollection_getAlignmentCount_WithSecondary_Secondary(self):
self.assertEqual(10, NGS.openReadCollection(WithSecondary).getAlignmentCount(Alignment.secondaryAlignment))
def test_ReadCollection_getAlignmentCount_WithSecondary_All(self):
self.assertEqual(178, NGS.openReadCollection(WithSecondary).getAlignmentCount(Alignment.all))
def test_ReadCollection_getAlignmentCount_PrimaryOnly_Secondary(self):
self.assertEqual(0, NGS.openReadCollection(PrimaryOnly).getAlignmentCount(Alignment.secondaryAlignment))
def test_ReadCollection_getAlignmentCount_PrimaryOnly_All(self):
self.assertEqual(3987701, NGS.openReadCollection(PrimaryOnly).getAlignmentCount(Alignment.all))
def test_ReadCollection_getAlignments_all(self):
alIt = NGS.openReadCollection(PrimaryOnly).getAlignments(Alignment.all)
def test_ReadCollection_getAlignments_Secondary(self):
alIt = NGS.openReadCollection(PrimaryOnly).getAlignments(Alignment.secondaryAlignment)
def test_ReadCollection_getAlignment(self):
al = NGS.openReadCollection(PrimaryOnly).getAlignment(PrimaryOnly + ".PA.1")
def test_ReadCollection_hasReference(self):
assert ( NGS.openReadCollection(PrimaryOnly).hasReference("supercont2.1") )
assert ( not NGS.openReadCollection(PrimaryOnly).hasReference("non-existent acc") )
def test_ReadCollection_getReference(self):
ref = NGS.openReadCollection(PrimaryOnly).getReference("supercont2.1")