def setUp(self):
self.parmsfile = "/Users/aragaven/PycharmProjects/biobrewlite/tests/test_rnaseq_workflow/test_run.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.parse_prog_info()
self.wrapper_name = 'salmon'
self.salmon_test = wr.SalmonCounts(self.wrapper_name, "test_samp",
*self.rw1.progs['salmon'],
**dict(self.rw1.base_kwargs))
def setUp(self):
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.parse_prog_info()
self.wrapper_name = 'salmon'
self.salmon_test = wr.SalmonCounts(self.wrapper_name, "test_samp",
*self.rw1.progs['salmon'],
**dict(self.rw1.base_kwargs))
def setUp(self):
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
self.wrapper_name = 'bammarkduplicates2'
self.biobambammarkdup_test = wr.BiobambamMarkDup(
self.wrapper_name,
"test_samp",
stdout=os.path.join(self.rw1.log_dir, 'bammarkduplicates.log'),
**dict(self.rw1.base_kwargs))
def setUp(self):
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
self.wrapper_name = 'picard_CollectWgsMetrics'
self.add_args = self.rw1.progs[self.wrapper_name]
#use *self.add_args to unroll the list
self.picard_test = wr.Picard(self.wrapper_name, "test_samp",
*self.add_args,
**dict(self.rw1.base_kwargs))
def setUp(self):
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
# self.rw1.parse_prog_info()
self.wrapper_name = 'qualimap_bamqc'
self.rw1.update_job_parms(self.wrapper_name)
new_base_kwargs = self.rw1.update_prog_suffixes(self.wrapper_name)
self.add_args = self.rw1.progs[self.wrapper_name]
self.qualimap_test = wr.QualiMap(self.wrapper_name,
"test_samp", *self.add_args,
**dict(new_base_kwargs))
def setUp(self):
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
self.wrapper_name = 'bammarkduplicates2'
self.rw1.update_job_parms(self.wrapper_name)
new_base_kwargs = self.rw1.update_prog_suffixes(self.wrapper_name)
self.biobambammarkdup_test = wr.Biobambam(self.wrapper_name,
"test_samp",
**dict(new_base_kwargs))
def setUp(self):
self.parmsfile = "/Users/aragaven/PycharmProjects/biobrewlite/tests/test_rnaseq_workflow/test_run.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
self.wrapper_name = 'bammarkduplicates2'
self.biobambammarkdup_test = wr.BiobambamMarkDup(
self.wrapper_name,
"test_samp",
stdout=os.path.join(self.rw1.log_dir, 'bammarkduplicates.log'),
**dict(self.rw1.base_kwargs))
def setUp(self):
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
self.wrapper_name = 'htseq-count'
self.add_args = self.rw1.progs[self.wrapper_name]
new_base_kwargs = self.rw1.update_prog_suffixes(self.wrapper_name)
self.htseq_test = wr.HtSeqCounts(self.wrapper_name,
"test_samp", *self.add_args,
**dict(new_base_kwargs))
def setUp(self):
self.wrapper_name = "fastqc"
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
self.wrapper_name = 'fastqc'
self.rw1.update_job_parms(self.wrapper_name)
new_base_kwargs = self.rw1.update_prog_suffixes(self.wrapper_name)
self.fastqc_test = wr.FastQC(self.wrapper_name, "test_samp",
**dict(new_base_kwargs))
def setUp(self):
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
# self.rw1.parse_prog_info()
self.wrapper_name = 'qualimap_bamqc'
self.add_args = self.rw1.progs[self.wrapper_name]
self.qualimap_test = wr.QualiMap(self.wrapper_name,
"test_samp",
*self.add_args,
stdout=os.path.join(
self.rw1.log_dir, 'qualimap.log'),
**dict(self.rw1.base_kwargs))
def setUp(self):
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
self.wrapper_name = 'gsnap'
self.add_args = self.rw1.progs[self.wrapper_name]
#use *self.add_args to unroll the list
self.rw1.update_job_parms(self.wrapper_name)
new_base_kwargs = self.rw1.update_prog_suffixes(self.wrapper_name)
self.gsnap_test = wr.Gsnap(self.wrapper_name, "test_samp",
*self.add_args, **dict(new_base_kwargs))
def setUp(self):
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.parse_prog_info()
self.wrapper_name = 'htseq-count'
self.htseq_test = wr.HtSeqCounts(self.wrapper_name,
"test_samp",
stdout=os.path.join(
self.rw1.run_parms['work_dir'],
self.rw1.run_parms['log_dir'],
'test_samp.log'),
**dict(self.rw1.base_kwargs))
def setUp(self):
self.wrapper_name = "fastqc"
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
self.wrapper_name = 'fastqc'
self.fastqc_test = wr.FastQC(self.wrapper_name,
"test_samp",
stdout_append=os.path.join(
self.rw1.log_dir,
'test_samp_fastqc.log'),
**dict(self.rw1.base_kwargs))
def setUp(self):
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
self.wrapper_name = 'samtools_index'
self.add_args = self.rw1.progs[self.wrapper_name]
# use *self.add_args to unroll the list
self.rw1.update_job_parms(self.wrapper_name)
new_base_kwargs = self.rw1.update_prog_suffixes(self.wrapper_name)
self.samtools_index_test = wr_samtools.SamTools(
self.wrapper_name + "_round_2", "test_samp", *self.add_args,
**dict(new_base_kwargs))
def setUp(self):
self.wrapper_name = "kneaddata"
self.parmsfile = "../test_metatranscriptome/test_run.yaml" # not made yet
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
self.wrapper_name = 'fastqc'
self.kneaddata_test = wr.Kneaddata(self.wrapper_name,
"test_samp",
stdout=os.path.join(
self.rw1.run_parms['work_dir'],
'fastqc.log'),
**dict(self.rw1.base_kwargs))
def setUp(self):
self.wrapper_name = "fastqc"
self.parmsfile = "/Users/aragaven/PycharmProjects/biobrewlite/tests/test_rnaseq_workflow/test_run.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
self.wrapper_name = 'fastqc'
self.fastqc_test = wr.FastQC(self.wrapper_name,
"test_samp",
stdout=os.path.join(
self.rw1.run_parms['work_dir'],
'fastqc.log'),
**dict(self.rw1.base_kwargs))
def setUp(self):
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
self.wrapper_name = 'bwa_mem'
self.add_args = self.rw1.progs[self.wrapper_name]
#use *self.add_args to unroll the list
new_base_kwargs = self.rw1.update_job_parms(self.wrapper_name)
self.bwa_test = wr.Bwa(self.wrapper_name,
"test_samp",
*self.add_args,
stdout=os.path.join(self.rw1.align_dir,
'bwa.sam'),
**dict(new_base_kwargs))
def setUp(self):
self.parmsfile = "/Users/aragaven/PycharmProjects/biobrewlite/tests/test_rnaseq_workflow/test_run.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
self.wrapper_name = 'gsnap'
self.add_args = self.rw1.progs[self.wrapper_name]
#use *self.add_args to unroll the list
new_base_kwargs = self.rw1.update_job_parms(self.wrapper_name)
self.gsnap_test = wr.Gsnap(self.wrapper_name,
"test_samp",
*self.add_args,
stdout=os.path.join(self.rw1.align_dir,
'gsnap.sam'),
**dict(new_base_kwargs))
def setUp(self):
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
self.wrapper_name = 'salmon_quant'
self.add_args = self.rw1.progs[self.wrapper_name]
# use *self.add_args to unroll the list
self.rw1.update_job_parms(self.wrapper_name)
new_base_kwargs = self.rw1.update_prog_suffixes(self.wrapper_name)
# self.bwa_test = wr.Bwa(self.wrapper_name, "test_samp", *self.add_args,
# **dict(new_base_kwargs))
self.salmon_test = wr.SalmonCounts(self.wrapper_name, "test_samp",
*self.add_args,
**dict(new_base_kwargs))
def setUp(self):
self.parmsfile = "test_run_mac_remote_pe_celegans.yaml"
self.rw1 = rsw(self.parmsfile)
def setUp(self):
self.parmsfile = "test_run_localhost_slurm_se_mus.yaml"
self.rw1 = rsw(self.parmsfile)
def setUp(self):
self.parmsfile = "test_run_sra_localhost_slurm_se_mus_spneumonia.yaml"
self.rw1 = rsw(self.parmsfile)
def setUp(self):
self.parmsfile = "test_run_localhost_slurm_pe_celegans.yaml"
self.rw1 = rsw(self.parmsfile)
def setUp(self):
self.parmsfile = "test_run_mac_remote_se_mus.yaml"
self.rw1 = rsw(self.parmsfile)
def setUp(self):
self.parmsfile = "test_wrappers_pe.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.paired_end = False
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()
def setUp(self):
self.wrapper_name = "qiime2"
self.parmsfile = "test_wrappers_qiime.yaml"
self.rw1 = rsw(self.parmsfile)
self.rw1.set_base_kwargs()
self.rw1.parse_prog_info()