def test_async_splitmapper_execution():
input = files.open(testfiles["reads_1.fastq"])
mappings = gem.splitmapper(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 test_async_splitmapper_execution():
input = files.open(testfiles["reads_1.fastq"])
mappings = gem.splitmapper(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 test_sync_splitmapper_execution():
gem.loglevel("debug")
input = files.open(testfiles["reads_1.fastq"])
mappings = gem.splitmapper(input, index, results_dir + "/splitmap_out.mapping")
assert mappings is not None
assert mappings.process is not None
assert mappings.filename == results_dir + "/splitmap_out.mapping"
assert os.path.exists(results_dir + "/splitmap_out.mapping")
assert sum(1 for x in mappings) == 10000
def test_sync_splitmapper_execution():
gem.loglevel("debug")
input = files.open(testfiles["reads_1.fastq"])
mappings = gem.splitmapper(input, index,
results_dir + "/splitmap_out.mapping")
assert mappings is not None
assert mappings.process is not None
assert mappings.filename == results_dir + "/splitmap_out.mapping"
assert os.path.exists(results_dir + "/splitmap_out.mapping")
assert sum(1 for x in mappings) == 10000
)
## we filter the junnctions now by their distance and
# write all junctions with a distance <= 500000 to a file
print "Writing junctions file"
gem.junctions.write_junctions(gem.junctions.filter_by_distance(junctions, 500000), junctions_out, index)
## Initial split map run with junction sites
# Here we take all unmapped reads after the denovo junction detection and
# pass them to the split mapper along with the junctions
print "Running initial split-map"
initial_split_mapping = gem.splitmapper(
gem.filter.unmapped(denovo_mapping),
index,
initial_split_out,
junctions_file=junctions_out,
mismatches=0.06,
threads=THREADS)
## Phase two, hard trim 20 bases from the right side
# and try mapping again
print "Running trim 20 mapping"
trim_20_mapping = gem.mapper(
gem.filter.unmapped(initial_split_mapping),
index,
trim_20_out,
trim=(0, 20), # this is the additional parameter to control the trimming
threads=THREADS)