def test_align_reads_snap(self):
configuration = {
'job_submitter': self.job_submitter,
'aligners': [self.aligners['snap']],
'samtools': self.samtools,
'output_folder': self.output_folder
}
expected_submit_job_calls = [
call(
'pbs',
"/path/to/snap paired output_folder/reference/snap 'NA|10831_ATCACG_L002_R1_001.fastq.gz' 'NA|10831_ATCACG_L002_R2_001.fastq.gz' -t 2 -b --TODO -o sam -",
{
'walltime': 6,
'args': '--fake-job-parameter -f |ake -j o|b -p arameter|',
'num_cpus': 2,
'name': 'nasp_snap_NA|10831_ATCACG_L002',
'queue': 'test|queue',
'mem_requested': 4,
'work_dir': 'output_folder/snap'
}, (('jobid', 'action'), ))
]
dispatcher._align_reads(self.assemblies['paired_pipe'], configuration,
self.index_job_id, self.reference)
dispatcher._submit_job.assert_has_calls(expected_submit_job_calls)
def test_align_reads_bwamem(self):
configuration = {
'job_submitter': self.job_submitter,
'aligners': [self.aligners['bwamem']],
'samtools': self.samtools,
'output_folder': self.output_folder
}
expected_submit_job_calls = [
call(
'pbs',
"/path/to/bwa mem -R '@RG\\tID:NA|10831_ATCACG_L002\\tSM:NA|10831_ATCACG_L002' -x '-k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0' -t 2 reference.fasta 'NA|10831_ATCACG_L002_R1_001.fastq.gz' 'NA|10831_ATCACG_L002_R2_001.fastq.gz'",
{
'work_dir': 'output_folder/bwamem',
'queue': 'test|queue',
'name': 'nasp_bwamem_NA|10831_ATCACG_L002',
'args': '--fake-job-parameter -f |ake -j o|b -p arameter|',
'walltime': 6,
'mem_requested': 4,
'num_cpus': 2
}, (('jobid', 'action'), )),
]
dispatcher._align_reads(self.assemblies['paired_pipe'], configuration,
self.index_job_id, self.reference)
dispatcher._submit_job.assert_has_calls(expected_submit_job_calls)
def test_align_reads_novoalign(self):
configuration = {
'job_submitter': self.job_submitter,
'aligners': [self.aligners['novoalign']],
'samtools': self.samtools,
'output_folder': self.output_folder
}
expected_submit_job_calls = [
call(
'pbs',
"/path/to/novoalign -d reference.fasta.idx -f 'NA|10831_ATCACG_L002_R1_001.fastq.gz' 'NA|10831_ATCACG_L002_R2_001.fastq.gz' -i PE 500,100 -c 2 -o SAM '@RG\\tID:NA|10831_ATCACG_L002\\tSM:NA|10831_ATCACG_L002' -K mismatch:stats.txt -i MP 99-99 99,99",
{
'name': 'nasp_novo_NA|10831_ATCACG_L002',
'queue': 'test|queue',
'mem_requested': 4,
'walltime': 6,
'num_cpus': 2,
'work_dir': 'output_folder/novo',
'args': '--fake-job-parameter -f |ake -j o|b -p arameter|'
}, (('jobid', 'action'), ))
]
dispatcher._align_reads(self.assemblies['paired_pipe'], configuration,
self.index_job_id, self.reference)
dispatcher._submit_job.assert_has_calls(expected_submit_job_calls)
def test_align_reads_bowtie2(self):
configuration = {
'job_submitter': self.job_submitter,
'aligners': [self.aligners['bowtie2']],
'samtools': self.samtools,
'output_folder': self.output_folder
}
expected_submit_job_calls = [
call(
'pbs',
"/path/to/bowtie2 --very-sensitive-local --un 'pipe|in|name.fastq.gz' --al 'space in name.fastq.gz' --threads 2 --rg 'SM:NA|10831_ATCACG_L002' --rg-id 'NA|10831_ATCACG_L002' -x reference -1 'NA|10831_ATCACG_L002_R1_001.fastq.gz' -2 'NA|10831_ATCACG_L002_R2_001.fastq.gz'",
{
'work_dir': 'output_folder/bowtie2',
'queue': 'test|queue',
'name': 'nasp_bowtie2_NA|10831_ATCACG_L002',
'args': '--fake-job-parameter -f |ake -j o|b -p arameter|',
'walltime': 6,
'mem_requested': 4,
'num_cpus': 2
}, (('jobid', 'action'), )),
]
dispatcher._align_reads(self.assemblies['paired_pipe'], configuration,
self.index_job_id, self.reference)
dispatcher._submit_job.assert_has_calls(expected_submit_job_calls)
def test_align_reads_snap(self):
configuration = {
'job_submitter': self.job_submitter,
'aligners': [ self.aligners['snap'] ],
'samtools': self.samtools,
'output_folder': self.output_folder
}
expected_submit_job_calls = [
call(
'pbs',
"/path/to/snap paired output_folder/reference/snap 'NA|10831_ATCACG_L002_R1_001.fastq.gz' 'NA|10831_ATCACG_L002_R2_001.fastq.gz' -t 2 -b --TODO -o sam -",
{'walltime': 6, 'args': '--fake-job-parameter -f |ake -j o|b -p arameter|', 'num_cpus': 2, 'name': 'nasp_snap_NA|10831_ATCACG_L002', 'queue': 'test|queue', 'mem_requested': 4, 'work_dir': 'output_folder/snap'},
(('jobid', 'action'),)
)
]
dispatcher._align_reads(self.assemblies['paired_pipe'], configuration, self.index_job_id, self.reference)
dispatcher._submit_job.assert_has_calls(expected_submit_job_calls)
def test_align_reads_novoalign(self):
configuration = {
'job_submitter': self.job_submitter,
'aligners': [ self.aligners['novoalign'] ],
'samtools': self.samtools,
'output_folder': self.output_folder
}
expected_submit_job_calls = [
call(
'pbs',
"/path/to/novoalign -d reference.fasta.idx -f 'NA|10831_ATCACG_L002_R1_001.fastq.gz' 'NA|10831_ATCACG_L002_R2_001.fastq.gz' -i PE 500,100 -c 2 -o SAM '@RG\\tID:NA|10831_ATCACG_L002\\tSM:NA|10831_ATCACG_L002' -K mismatch:stats.txt -i MP 99-99 99,99",
{'name': 'nasp_novo_NA|10831_ATCACG_L002', 'queue': 'test|queue', 'mem_requested': 4, 'walltime': 6, 'num_cpus': 2, 'work_dir': 'output_folder/novo', 'args': '--fake-job-parameter -f |ake -j o|b -p arameter|'},
(('jobid', 'action'),)
)
]
dispatcher._align_reads(self.assemblies['paired_pipe'], configuration, self.index_job_id, self.reference)
dispatcher._submit_job.assert_has_calls(expected_submit_job_calls)
def test_align_reads_bwamem(self):
configuration = {
'job_submitter': self.job_submitter,
'aligners': [ self.aligners['bwamem'] ],
'samtools': self.samtools,
'output_folder': self.output_folder
}
expected_submit_job_calls = [
call(
'pbs',
"/path/to/bwa mem -R '@RG\\tID:NA|10831_ATCACG_L002\\tSM:NA|10831_ATCACG_L002' -x '-k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0' -t 2 reference.fasta 'NA|10831_ATCACG_L002_R1_001.fastq.gz' 'NA|10831_ATCACG_L002_R2_001.fastq.gz'",
{'work_dir': 'output_folder/bwamem', 'queue': 'test|queue', 'name': 'nasp_bwamem_NA|10831_ATCACG_L002', 'args': '--fake-job-parameter -f |ake -j o|b -p arameter|', 'walltime': 6, 'mem_requested': 4, 'num_cpus': 2},
(('jobid', 'action'),)
),
]
dispatcher._align_reads(self.assemblies['paired_pipe'], configuration, self.index_job_id, self.reference)
dispatcher._submit_job.assert_has_calls(expected_submit_job_calls)
def test_align_reads_bowtie2(self):
configuration = {
'job_submitter': self.job_submitter,
'aligners': [ self.aligners['bowtie2'] ],
'samtools': self.samtools,
'output_folder': self.output_folder
}
expected_submit_job_calls = [
call(
'pbs',
"/path/to/bowtie2 --very-sensitive-local --un 'pipe|in|name.fastq.gz' --al 'space in name.fastq.gz' --threads 2 --rg 'SM:NA|10831_ATCACG_L002' --rg-id 'NA|10831_ATCACG_L002' -x reference -1 'NA|10831_ATCACG_L002_R1_001.fastq.gz' -2 'NA|10831_ATCACG_L002_R2_001.fastq.gz'",
{'work_dir': 'output_folder/bowtie2', 'queue': 'test|queue', 'name': 'nasp_bowtie2_NA|10831_ATCACG_L002', 'args': '--fake-job-parameter -f |ake -j o|b -p arameter|', 'walltime': 6, 'mem_requested': 4, 'num_cpus': 2},
(('jobid', 'action'),)
),
]
dispatcher._align_reads(self.assemblies['paired_pipe'], configuration, self.index_job_id, self.reference)
dispatcher._submit_job.assert_has_calls(expected_submit_job_calls)
