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
).merge(merge_out) # write to file
## remove files
if REMOVE_FILES:
print "Removing intermediate files"
os.remove(initial_out)
os.remove(initial_split_out)
os.remove(denovo_out)
os.remove(junctions_out)
os.remove(trim_20_out)
os.remove(trim_20_split_out)
## pair align the mappings
print "Running pair aligner"
paired_mapping = gem.pairalign(merged, index, paired_out, max_insert_size=100000, threads=THREADS)
if REMOVE_FILES:
os.remove(merge_out)
## validate and score the alignment
print "Validating and scoring alignment"
scored = gem.score(paired_mapping, index, final_out, threads=THREADS)
if REMOVE_FILES:
os.remove(paired_out)
## convert the result to sam and then to bam
print "Converting to sam"
sam = gem.gem2sam(scored, index, threads=4)
bam = gem.sam2bam(sam, sam_out, sorted=True)
