def test_async_mapper_execution():
input = files.open(testfiles["reads_1.fastq"])
mappings = gem.mapper(input, index)
assert mappings is not None
assert mappings.process is not None
assert mappings.filename is None
assert sum(1 for x in mappings) == 10000
def gem_mapping(gem_index_path, fastq_path, out_map_path, **kwargs):
"""
:param None focus: trims the sequence in the input FASTQ file according to a
(start, end) position, or the name of a restriction enzyme. By default it
uses the full sequence.
:param 33 quality: set it to 'ignore' in order to speed-up the mapping
"""
gem_index_path = os.path.abspath(os.path.expanduser(gem_index_path))
fastq_path = os.path.abspath(os.path.expanduser(fastq_path))
out_map_path = os.path.abspath(os.path.expanduser(out_map_path))
nthreads = kwargs.get('nthreads' , 8)
max_edit_distance = kwargs.get('max_edit_distance' , 0.04)
mismatches = kwargs.get('mismatches' , 0.04)
quality = kwargs.get('quality' , 33)
# check kwargs
for kw in kwargs:
if not kw in ['nthreads', 'max_edit_distance',
'mismatches', 'max_reads_per_chunk',
'out_files', 'temp_dir']:
warn('WARNING: %s not is usual keywords, misspelled?' % kw)
# input
inputf = gem.files.open(fastq_path)
# mapping
print 'TO GEM', fastq_path
return gem.mapper(inputf, gem_index_path, min_decoded_strata=0,
max_decoded_matches=1, unique_mapping=False,
max_edit_distance=max_edit_distance,
mismatches=mismatches, quality=quality,
output=out_map_path,
threads=nthreads)
def test_quality_pass_on_execution():
input = files.open(testfiles["reads_1.fastq"])
mappings = gem.mapper(input,
index,
output=results_dir + "/quality_passon_mapping.map")
assert mappings.quality == "offset-33", "Quality should be 'offset-33' but is %s" % (
str(mappings.quality))
def test_interleaved_pair_aligner_run():
input1 = files.open(testfiles["reads_1.fastq"])
input2 = files.open(testfiles["reads_2.fastq"])
mappings = gem.mapper(filter.interleave([input1, input2]), index)
paired = gem.pairalign(mappings, index)
assert paired is not None
assert sum(1 for x in paired) == 20000 # test dataset does not pair at all
def test_interleaved_pair_aligner_run():
input1 = files.open(testfiles["reads_1.fastq"])
input2 = files.open(testfiles["reads_2.fastq"])
mappings = gem.mapper(filter.interleave([input1, input2]), index)
paired = gem.pairalign(mappings, index)
assert paired is not None
assert sum(1 for x in paired) == 20000 # test dataset does not pair at all
def test_async_mapper_execution():
input = files.open(testfiles["reads_1.fastq"])
mappings = gem.mapper(input, index)
assert mappings is not None
assert mappings.process is not None
assert mappings.filename is None
assert sum(1 for x in mappings) == 10000
def gem_mapping(gem_index_path, fastq_path, out_map_path, **kwargs):
"""
:param None focus: trims the sequence in the input FASTQ file according to a
(start, end) position, or the name of a restriction enzyme. By default it
uses the full sequence.
:param 33 quality: set it to 'ignore' in order to speed-up the mapping
"""
gem_index_path = os.path.abspath(os.path.expanduser(gem_index_path))
fastq_path = os.path.abspath(os.path.expanduser(fastq_path))
out_map_path = os.path.abspath(os.path.expanduser(out_map_path))
nthreads = kwargs.get('nthreads' , 8)
max_edit_distance = kwargs.get('max_edit_distance' , 0.04)
mismatches = kwargs.get('mismatches' , 0.04)
quality = kwargs.get('quality' , 33)
# check kwargs
for kw in kwargs:
if not kw in ['nthreads', 'max_edit_distance',
'mismatches', 'max_reads_per_chunk',
'out_files', 'temp_dir']:
warn('WARNING: %s not is usual keywords, misspelled?' % kw)
# input
inputf = gem.files.open(fastq_path)
# mapping
print 'TO GEM', fastq_path
return gem.mapper(inputf, gem_index_path, min_decoded_strata=0,
max_decoded_matches=1, unique_mapping=False,
max_edit_distance=max_edit_distance,
mismatches=mismatches, quality=quality,
output=out_map_path,
threads=nthreads)
def test_sync_mapper_execution():
input = files.open(testfiles["reads_1.fastq"])
mappings = gem.mapper(input, index, results_dir + "/result.mapping")
assert mappings is not None
assert mappings.process is not None
assert mappings.filename is not None
assert mappings.filename == results_dir + "/result.mapping"
assert sum(1 for x in mappings) == 10000
def test_sync_mapper_execution():
input = files.open(testfiles["reads_1.fastq"])
mappings = gem.mapper(input, index, results_dir + "/result.mapping")
assert mappings is not None
assert mappings.process is not None
assert mappings.filename is not None
assert mappings.filename == results_dir + "/result.mapping"
assert sum(1 for x in mappings) == 10000
def test_gem2sam_execution_to_file():
input = gem.files.open(testfiles["reads_1.fastq"])
mappings = gem.mapper(input, index)
result = results_dir + "/test_sam.sam"
sam = gem.gem2sam(mappings, index, output=result, compact=True)
assert sam is not None
assert sam.process is not None
assert sam.filename == result
assert os.path.exists(result)
def test_interleaved_mapper_run():
input1 = files.open(testfiles["reads_1.fastq"])
input2 = files.open(testfiles["reads_2.fastq"])
mappings = gem.mapper(filter.interleave([input1, input2]), index)
assert mappings is not None
assert mappings.process is not None
assert mappings.filename is None
assert sum(1 for x in mappings) == 20000
def test_gem2sam_execution_to_file():
input = gem.files.open(testfiles["reads_1.fastq"])
mappings = gem.mapper(input, index)
result = results_dir + "/test_sam.sam"
sam = gem.gem2sam(mappings, index, output=result, compact=True)
assert sam is not None
assert sam.process is not None
assert sam.filename == result
assert os.path.exists(result)
def test_interleaved_mapper_run():
input1 = files.open(testfiles["reads_1.fastq"])
input2 = files.open(testfiles["reads_2.fastq"])
mappings = gem.mapper(filter.interleave([input1, input2]), index)
assert mappings is not None
assert mappings.process is not None
assert mappings.filename is None
assert sum(1 for x in mappings) == 20000
def test_gem2sam_sam2bam():
input = gem.files.open(testfiles["reads_1.fastq"])
mappings = gem.mapper(input, index)
sam = gem.gem2sam(mappings, index, compact=True)
result = results_dir + "/test_sam.bam"
bam = gem.sam2bam(sam, output=result)
assert os.path.exists(result)
count = 0
for l in gem.files.open(result):
count += 1
assert count == 10000, "Count 10000!=%d" % count
def test_gem2sam_execution():
input = files.open(testfiles["reads_1.fastq"])
mappings = gem.mapper(input, index)
sam = gem.gem2sam(mappings, index, compact=True)
assert sam is not None
assert sam.process is not None
assert sam.filename is None
count = 0
for read in sam:
count += 1
assert count == 10000
def test_gem2sam_execution():
input = files.open(testfiles["reads_1.fastq"])
mappings = gem.mapper(input, index)
sam = gem.gem2sam(mappings, index, compact=True)
assert sam is not None
assert sam.process is not None
assert sam.filename is None
count = 0
for read in sam:
count += 1
assert count == 10000
def test_gem2sam_sam2bam():
input = gem.files.open(testfiles["reads_1.fastq"])
mappings = gem.mapper(input, index)
sam = gem.gem2sam(mappings, index, compact=True)
result = results_dir+"/test_sam.bam"
bam = gem.sam2bam(sam, output=result)
assert os.path.exists(result)
count = 0
for l in gem.files.open(result):
count += 1
assert count == 10000, "Count 10000!=%d" % count
def test_quality_pass_on_execution():
input = files.open(testfiles["reads_1.fastq"])
mappings = gem.mapper(input, index, output=results_dir+"/quality_passon_mapping.map")
assert mappings.quality == "offset-33", "Quality should be 'offset-33' but is %s" % (str(mappings.quality))
# output
local_out_sam = out_sam_path + '.%d:%d-%d' % (
N_WINDOWS - len(range_stop), seq_beg, seq_end)
out_files.append(local_out_sam)
# input
inputf = gem.files.open(fastq_path)
# trimming
trimmed = gem.filter.run_filter(
inputf, ['--hard-trim', '%d,%d' % (trim_5, trim_3)],
threads=nthreads, paired=not single_end)
# mapping
mapped = gem.mapper(trimmed, gem_index_path, min_decoded_strata=0,
max_decoded_matches=2, unique_mapping=False,
max_edit_distance=max_edit_distance,
mismatches=mismatches,
output=temp_dir + '/test.map',
threads=nthreads)
# convert to sam/bam
if output_is_bam:
sam = gem.gem2sam(mapped, index=gem_index_path, threads=nthreads,
single_end=single_end)
_ = gem.sam2bam(sam, output=local_out_sam, threads=nthreads)
else:
sam = gem.gem2sam(mapped, index=gem_index_path, output=local_out_sam,
threads=nthreads, single_end=single_end)
# Recursively go to the next iteration.
unmapped_fastq_path = os.path.split(fastq_path)[1]
if unmapped_fastq_path[-1].isdigit():
# output
local_out_sam = out_sam_path + '.%d' % (seq_len)
out_files.append(local_out_sam)
# input
inputf = gem.files.open(fastq_path)
# trimming
trimmed = gem.filter.run_filter(
inputf, ['--hard-trim', '%d,%d' % (trim_5, trim_3)],
threads=nthreads, paired=not single_end)
# mapping
mapped = gem.mapper(trimmed, gem_index_path, min_decoded_strata=0,
max_decoded_matches=2, unique_mapping=False,
max_edit_distance=max_edit_distance,
mismatches=mismatches,
output=temp_dir + '/test.map',
threads=nthreads)
# convert to sam
sam = gem.gem2sam(mapped, index=gem_index_path, output=local_out_sam,
threads=nthreads, single_end=single_end)
if output_is_bam:
sam = gem.gem2sam(mapped, index=gem_index_path, threads=nthreads,
single_end=single_end)
_ = gem.sam2bam(sam, output=local_out_sam, threads=nthreads)
else:
sam = gem.gem2sam(mapped, index=gem_index_path, output=local_out_sam,
threads=nthreads, single_end=single_end)
# Recursively go to the next iteration.
def iterative_mapping(gem_index_path, fastq_path, out_sam_path,
range_start, range_stop, **kwargs):
"""
Map iteratively a given FASTQ file to a reference genome.
:param gem_index_path: path to index file created from a reference genome
using gem-index tool
:param fastq_path: PATH to fastq file, either compressed or not.
:param out_sam_path: path to a directory where to store mapped reads in SAM/
BAM format (see option output_is_bam).
:param range_start: list of integers representing the start position of each
read fragment to be mapped (starting at 1 includes the first nucleotide
of the read).
:param range_stop: list of integers representing the end position of each
read fragment to be mapped.
:param True single_end: when FASTQ contains paired-ends flags
:param 4 nthreads: number of threads to use for mapping (number of CPUs)
:param 0.04 max_edit_distance: The maximum number of edit operations allowed
while verifying candidate matches by dynamic programming.
:param 0.04 mismatches: The maximum number of nucleotide substitutions
allowed while mapping each k-mer. It is always guaranteed that, however
other options are chosen, all the matches up to the specified number of
substitutions will be found by the program.
:param -1 max_reads_per_chunk: maximum number of reads to process at a time.
If -1, all reads will be processed in one run (more RAM memory needed).
:param False output_is_bam: Use binary (compressed) form of generated
out-files with mapped reads (recommended to save disk space).
:param /tmp temp_dir: important to change. Intermediate FASTQ files will be
written there.
:returns: a list of paths to generated outfiles. To be passed to
:func:`pytadbit.parsers.sam_parser.parse_sam`
"""
gem_index_path = os.path.abspath(os.path.expanduser(gem_index_path))
fastq_path = os.path.abspath(os.path.expanduser(fastq_path))
out_sam_path = os.path.abspath(os.path.expanduser(out_sam_path))
single_end = kwargs.get('single_end' , True)
max_edit_distance = kwargs.get('max_edit_distance' , 0.04)
mismatches = kwargs.get('mismatches' , 0.04)
nthreads = kwargs.get('nthreads' , 4)
max_reads_per_chunk = kwargs.get('max_reads_per_chunk' , -1)
out_files = kwargs.get('out_files' , [])
output_is_bam = kwargs.get('output_is_bam' , False)
temp_dir = os.path.abspath(os.path.expanduser(
kwargs.get('temp_dir', tempfile.gettempdir())))
# check kwargs
for kw in kwargs:
if not kw in ['single_end', 'nthreads', 'max_edit_distance',
'mismatches', 'max_reads_per_chunk',
'out_files', 'output_is_bam', 'temp_dir']:
warn('WARNING: %s not is usual keywords, misspelled?' % kw)
# check windows:
if not isinstance(range_start, list) or not isinstance(range_stop, list):
if (not isinstance(range_start, tuple) or
not isinstance(range_stop, tuple)):
raise Exception('ERROR: range_start and range_stop should be lists')
range_start = list(range_start)
range_stop = list(range_stop)
if (not all(isinstance(i, int) for i in range_start) or
not all(isinstance(i, int) for i in range_stop)):
try:
range_start = map(int, range_start)
range_stop = map(int, range_stop)
warn('WARNING: range_start and range_stop converted to integers')
except ValueError:
raise Exception('ERROR: range_start and range_stop should contain' +
' integers only')
if (len(zip(range_start, range_stop)) < len(range_start) or
len(range_start) != len(range_stop)):
raise Exception('ERROR: range_start and range_stop should have the ' +
'same sizes and windows should be uniques.')
if any([i >= j for i, j in zip(range_start, range_stop)]):
raise Exception('ERROR: start positions should always be lower than ' +
'stop positions.')
if any([i <= 0 for i in range_start]):
raise Exception('ERROR: start positions should be strictly positive.')
# create directories
for rep in [temp_dir, os.path.split(out_sam_path)[0]]:
mkdir(rep)
#get the length of a read
if fastq_path.endswith('.gz'):
fastqh = gzip.open(fastq_path)
else:
fastqh = open(fastq_path)
# get the length from the length of the second line, which is the sequence
# can not use the "length" keyword, as it is not always present
try:
_ = fastqh.next()
raw_seq_len = len(fastqh.next().strip())
fastqh.close()
except StopIteration:
raise IOError('ERROR: problem reading %s\n' % fastq_path)
if not N_WINDOWS:
N_WINDOWS = len(range_start)
# Split input files if required and apply iterative mapping to each
# segment separately.
if max_reads_per_chunk > 0:
kwargs['max_reads_per_chunk'] = -1
print 'Split input file %s into chunks' % fastq_path
chunked_files = _chunk_file(
fastq_path,
os.path.join(temp_dir, os.path.split(fastq_path)[1]),
max_reads_per_chunk * 4)
print '%d chunks obtained' % len(chunked_files)
for i, fastq_chunk_path in enumerate(chunked_files):
global N_WINDOWS
N_WINDOWS = 0
print 'Run iterative_mapping recursively on %s' % fastq_chunk_path
out_files.extend(iterative_mapping(
gem_index_path, fastq_chunk_path,
out_sam_path + '.%d' % (i + 1), range_start[:], range_stop[:],
**kwargs))
for i, fastq_chunk_path in enumerate(chunked_files):
# Delete chunks only if the file was really chunked.
if len(chunked_files) > 1:
print 'Remove the chunks: %s' % ' '.join(chunked_files)
os.remove(fastq_chunk_path)
return out_files
# end position according to sequence in the file
# removes 1 in order to start at 1 instead of 0
try:
seq_end = range_stop.pop(0)
seq_beg = range_start.pop(0)
except IndexError:
return out_files
# define what we trim
seq_len = seq_end - seq_beg
trim_5, trim_3 = trimming(raw_seq_len, seq_beg - 1, seq_len - 1)
# output
local_out_sam = out_sam_path + '.%d:%d-%d' % (
N_WINDOWS - len(range_stop), seq_beg, seq_end)
out_files.append(local_out_sam)
# input
inputf = gem.files.open(fastq_path)
# trimming
trimmed = gem.filter.run_filter(
inputf, ['--hard-trim', '%d,%d' % (trim_5, trim_3)],
threads=nthreads, paired=not single_end)
# mapping
mapped = gem.mapper(trimmed, gem_index_path, min_decoded_strata=0,
max_decoded_matches=2, unique_mapping=False,
max_edit_distance=max_edit_distance,
mismatches=mismatches,
output=temp_dir + '/test.map',
threads=nthreads)
# convert to sam/bam
if output_is_bam:
sam = gem.gem2sam(mapped, index=gem_index_path, threads=nthreads,
single_end=single_end)
_ = gem.sam2bam(sam, output=local_out_sam, threads=nthreads)
else:
sam = gem.gem2sam(mapped, index=gem_index_path, output=local_out_sam,
threads=nthreads, single_end=single_end)
# Recursively go to the next iteration.
unmapped_fastq_path = os.path.split(fastq_path)[1]
if unmapped_fastq_path[-1].isdigit():
unmapped_fastq_path = unmapped_fastq_path.rsplit('.', 1)[0]
unmapped_fastq_path = os.path.join(
temp_dir, unmapped_fastq_path + '.%d:%d-%d' % (
N_WINDOWS - len(range_stop), seq_beg, seq_end))
_filter_unmapped_fastq(fastq_path, local_out_sam, unmapped_fastq_path)
out_files.extend(iterative_mapping(gem_index_path, unmapped_fastq_path,
out_sam_path,
range_start, range_stop, **kwargs))
os.remove(unmapped_fastq_path)
return out_files
def iterative_mapping(gem_index_path, fastq_path, out_sam_path, range_start,
range_stop, **kwargs):
"""
Map iteratively a given FASTQ file to a reference genome.
:param gem_index_path: path to index file created from a reference genome
using gem-index tool
:param fastq_path: PATH to fastq file, either compressed or not.
:param out_sam_path: path to a directory where to store mapped reads in SAM/
BAM format (see option output_is_bam).
:param range_start: list of integers representing the start position of each
read fragment to be mapped (starting at 1 includes the first nucleotide
of the read).
:param range_stop: list of integers representing the end position of each
read fragment to be mapped.
:param True single_end: when FASTQ contains paired-ends flags
:param 4 nthreads: number of threads to use for mapping (number of CPUs)
:param 0.04 max_edit_distance: The maximum number of edit operations allowed
while verifying candidate matches by dynamic programming.
:param 0.04 mismatches: The maximum number of nucleotide substitutions
allowed while mapping each k-mer. It is always guaranteed that, however
other options are chosen, all the matches up to the specified number of
substitutions will be found by the program.
:param -1 max_reads_per_chunk: maximum number of reads to process at a time.
If -1, all reads will be processed in one run (more RAM memory needed).
:param False output_is_bam: Use binary (compressed) form of generated
out-files with mapped reads (recommended to save disk space).
:param /tmp temp_dir: important to change. Intermediate FASTQ files will be
written there.
:returns: a list of paths to generated outfiles. To be passed to
:func:`pytadbit.parsers.sam_parser.parse_sam`
"""
gem_index_path = os.path.abspath(os.path.expanduser(gem_index_path))
fastq_path = os.path.abspath(os.path.expanduser(fastq_path))
out_sam_path = os.path.abspath(os.path.expanduser(out_sam_path))
single_end = kwargs.get('single_end', True)
max_edit_distance = kwargs.get('max_edit_distance', 0.04)
mismatches = kwargs.get('mismatches', 0.04)
nthreads = kwargs.get('nthreads', 4)
max_reads_per_chunk = kwargs.get('max_reads_per_chunk', -1)
out_files = kwargs.get('out_files', [])
output_is_bam = kwargs.get('output_is_bam', False)
temp_dir = os.path.abspath(
os.path.expanduser(kwargs.get('temp_dir', tempfile.gettempdir())))
# check kwargs
for kw in kwargs:
if not kw in [
'single_end', 'nthreads', 'max_edit_distance', 'mismatches',
'max_reads_per_chunk', 'out_files', 'output_is_bam', 'temp_dir'
]:
warn('WARNING: %s not is usual keywords, misspelled?' % kw)
# check windows:
if not isinstance(range_start, list) or not isinstance(range_stop, list):
if (not isinstance(range_start, tuple)
or not isinstance(range_stop, tuple)):
raise Exception(
'ERROR: range_start and range_stop should be lists')
range_start = list(range_start)
range_stop = list(range_stop)
if (not all(isinstance(i, int) for i in range_start)
or not all(isinstance(i, int) for i in range_stop)):
try:
range_start = map(int, range_start)
range_stop = map(int, range_stop)
warn('WARNING: range_start and range_stop converted to integers')
except ValueError:
raise Exception(
'ERROR: range_start and range_stop should contain' +
' integers only')
if (len(zip(range_start, range_stop)) < len(range_start)
or len(range_start) != len(range_stop)):
raise Exception('ERROR: range_start and range_stop should have the ' +
'same sizes and windows should be uniques.')
if any([i >= j for i, j in zip(range_start, range_stop)]):
raise Exception('ERROR: start positions should always be lower than ' +
'stop positions.')
if any([i <= 0 for i in range_start]):
raise Exception('ERROR: start positions should be strictly positive.')
# create directories
for rep in [temp_dir, os.path.split(out_sam_path)[0]]:
mkdir(rep)
#get the length of a read
if fastq_path.endswith('.gz'):
fastqh = gzip.open(fastq_path)
else:
fastqh = open(fastq_path)
# get the length from the length of the second line, which is the sequence
# can not use the "length" keyword, as it is not always present
try:
_ = fastqh.next()
raw_seq_len = len(fastqh.next().strip())
fastqh.close()
except StopIteration:
raise IOError('ERROR: problem reading %s\n' % fastq_path)
if not N_WINDOWS:
N_WINDOWS = len(range_start)
# Split input files if required and apply iterative mapping to each
# segment separately.
if max_reads_per_chunk > 0:
kwargs['max_reads_per_chunk'] = -1
print 'Split input file %s into chunks' % fastq_path
chunked_files = _chunk_file(
fastq_path, os.path.join(temp_dir,
os.path.split(fastq_path)[1]),
max_reads_per_chunk * 4)
print '%d chunks obtained' % len(chunked_files)
for i, fastq_chunk_path in enumerate(chunked_files):
global N_WINDOWS
N_WINDOWS = 0
print 'Run iterative_mapping recursively on %s' % fastq_chunk_path
out_files.extend(
iterative_mapping(gem_index_path, fastq_chunk_path,
out_sam_path + '.%d' % (i + 1),
range_start[:], range_stop[:], **kwargs))
for i, fastq_chunk_path in enumerate(chunked_files):
# Delete chunks only if the file was really chunked.
if len(chunked_files) > 1:
print 'Remove the chunks: %s' % ' '.join(chunked_files)
os.remove(fastq_chunk_path)
return out_files
# end position according to sequence in the file
# removes 1 in order to start at 1 instead of 0
try:
seq_end = range_stop.pop(0)
seq_beg = range_start.pop(0)
except IndexError:
return out_files
# define what we trim
seq_len = seq_end - seq_beg
trim_5, trim_3 = trimming(raw_seq_len, seq_beg - 1, seq_len - 1)
# output
local_out_sam = out_sam_path + '.%d:%d-%d' % (N_WINDOWS - len(range_stop),
seq_beg, seq_end)
out_files.append(local_out_sam)
# input
inputf = gem.files.open(fastq_path)
# trimming
trimmed = gem.filter.run_filter(
inputf, ['--hard-trim', '%d,%d' % (trim_5, trim_3)],
threads=nthreads,
paired=not single_end)
# mapping
mapped = gem.mapper(trimmed,
gem_index_path,
min_decoded_strata=0,
max_decoded_matches=2,
unique_mapping=False,
max_edit_distance=max_edit_distance,
mismatches=mismatches,
output=temp_dir + '/test.map',
threads=nthreads)
# convert to sam/bam
if output_is_bam:
sam = gem.gem2sam(mapped,
index=gem_index_path,
threads=nthreads,
single_end=single_end)
_ = gem.sam2bam(sam, output=local_out_sam, threads=nthreads)
else:
sam = gem.gem2sam(mapped,
index=gem_index_path,
output=local_out_sam,
threads=nthreads,
single_end=single_end)
# Recursively go to the next iteration.
unmapped_fastq_path = os.path.split(fastq_path)[1]
if unmapped_fastq_path[-1].isdigit():
unmapped_fastq_path = unmapped_fastq_path.rsplit('.', 1)[0]
unmapped_fastq_path = os.path.join(
temp_dir, unmapped_fastq_path + '.%d:%d-%d' %
(N_WINDOWS - len(range_stop), seq_beg, seq_end))
_filter_unmapped_fastq(fastq_path, local_out_sam, unmapped_fastq_path)
out_files.extend(
iterative_mapping(gem_index_path, unmapped_fastq_path, out_sam_path,
range_start, range_stop, **kwargs))
os.remove(unmapped_fastq_path)
return out_files
paired_out = "%s_paired.map" % name
# scored mappings
final_out = "%s.map" % name
# sam/bam output
sam_out = "%s.bam" % name
## Create initial mapping
# we deal with a single file with interleaved paired reads here, but
# creating input from two files for the read pairs is straight forward using the interleave filter
#
# input_1 = gem.files.open(input_file)
# input_2 = gem.files.open(input_file2)
# input = gem.filter.interleave([input_1, input_2])
print "Running initial mapping"
input = gem.files.open(reads)
initial_mapping = gem.mapper(input, index, initial_out, mismatches=0.07, delta=1, threads=THREADS)
## junction sites
# before we can do the split mapping, we have to load
# the junction sites from a gtf annotation and
# run the denovo-junction detection. This will also give
# us a mapping that preserves short indels detected during the
# extraction run.
print "Loading GTF junctions from %s" % annotation
junctions = gem.junctions.from_gtf(annotation)
# now the denovo run. This returns a tuple : (mapping, junctions)
# and here we use the merge_with parameter to merge the denovo junctions with
# the previously loaded gtf junctions.
#
# Also note that we pass only unmapped reads from the initial mapping to the junction
