def initialize_project(self):
'''Wrapper for building the project.
1. Load the settings
2. Load the assembly
3. Load the samples
4. Set the directory structure
'''
self.logger.info('Project Name: {0.name}'.format(self))
# Settings
self.settings = PipelineSettings(self.args, self.PATH)
self.logger.info('Baseline Threads: {0.threads}'.format(self.settings))
self.logger.info('Clip Adapters: {0.clipping}'.format(self.settings))
if self.settings.clipping:
self.logger.info('Minimum read length: {0.min_length}'.format(
self.settings))
self.logger.info('Minimum MAPQ: {0.min_map_q}'.format(self.settings))
self.logger.info('Aligners: {0}'.format(self.settings.aln_list))
self.logger.info('Somatic Mutation Detectors: {0}'.format(
self.settings.smd_list))
# Assembly info
self._set_assembly()
self.logger.info('Reference Name: {0}'.format(
self.assembly['refname']))
# Samples
self.samples.load_samples(os.path.abspath(self.args.metadata),
self.PATH, self.name)
# File structure
self._set_project_files()
def initialize_project(self):
"""Wrapper for building the project.
1. Load the settings
2. Load the assembly
3. Load the samples
4. Set the directory structure
"""
self.logger.info("Project Name: {0.name}".format(self))
# Settings
self.settings = PipelineSettings(self.args, self.PATH)
self.logger.info("Baseline Threads: {0.threads}".format(self.settings))
self.logger.info("Clip Adapters: {0.clipping}".format(self.settings))
if self.settings.clipping:
self.logger.info("Minimum read length: {0.min_length}".format(self.settings))
self.logger.info("Minimum MAPQ: {0.min_map_q}".format(self.settings))
self.logger.info("Aligners: {0}".format(self.settings.aln_list))
self.logger.info("Somatic Mutation Detectors: {0}".format(self.settings.smd_list))
# Assembly info
self._set_assembly()
self.logger.info("Reference Name: {0}".format(self.assembly["refname"]))
# Samples
self.samples.load_samples(os.path.abspath(self.args.metadata), self.PATH, self.name)
# File structure
self._set_project_files()
class Project(object):
'''Object representing a Tumor/Normal Exome Project
-- args - the argparser object
-- PATH - the path to the ExScaliburSMD application directory
-- assembly - the assembly dictionary from the assembly yaml file
-- settings - the PipelineSettings object
-- files - dictionary of main project paths
-- samples - the SampleFactory object
-- name - the project ID
'''
def __init__(self, args, PATH):
self.logger = logging.getLogger('SMD.Project')
self.args = args
self.PATH = PATH
self.assembly = None
self.settings = None
self.files = None
self.name = args.project_id
self.samples = SampleFactory()
self.final_reporter_yaml = None
self.bds_file = None
# Lists holding the job submission commands to write to the
# submission scripts
self.preprocessing_jobs = []
self.alignments_jobs = []
self.gatk_jobs = []
self.somatic_jobs = []
self.annotation_jobs = []
self.report_jobs = []
self.config_list = []
def initialize_project(self):
'''Wrapper for building the project.
1. Load the settings
2. Load the assembly
3. Load the samples
4. Set the directory structure
'''
self.logger.info('Project Name: {0.name}'.format(self))
# Settings
self.settings = PipelineSettings(self.args, self.PATH)
self.logger.info('Baseline Threads: {0.threads}'.format(self.settings))
self.logger.info('Clip Adapters: {0.clipping}'.format(self.settings))
if self.settings.clipping:
self.logger.info('Minimum read length: {0.min_length}'.format(
self.settings))
self.logger.info('Minimum MAPQ: {0.min_map_q}'.format(self.settings))
self.logger.info('Aligners: {0}'.format(self.settings.aln_list))
self.logger.info('Somatic Mutation Detectors: {0}'.format(
self.settings.smd_list))
# Assembly info
self._set_assembly()
self.logger.info('Reference Name: {0}'.format(
self.assembly['refname']))
# Samples
self.samples.load_samples(os.path.abspath(self.args.metadata),
self.PATH, self.name)
# File structure
self._set_project_files()
def configure_pipeline(self):
'''Wrapper for creating the configuration files for each sample'''
self.settings.write_settings_cfg(self)
for s in self.samples:
s.write_sample_bds(self, self.settings)
s.write_sample_report_yaml()
self.config_list.append(s.sample_cfg)
self.__write_reporter_yaml()
self.__write_bds_config()
self.__write_project_run_script()
def _set_assembly(self):
'''Grabs the yaml file, validates it, and returns the dictionary'''
# Load
in_fh = open(self.args.config_file, 'rU')
chk = yaml.safe_load(in_fh)['reference']
in_fh.close()
# Check the file
refname = chk.keys()[0]
required = [
'cosmic', 'exons_bed', 'knowndb', 'knownindel', 'referenceseq',
'sequence_dictionary'
]
if 'novoalign' in self.settings.aln_list:
required.append('novoalign_index')
for i in required:
assert i in chk[refname], self.logger.error(
"Required refrence section '%s' missing" % i)
if i in [
'cosmic', 'exons_bed', 'knowndb', 'knownindel',
'referenceseq', 'sequence_dictionary'
]:
try:
fp = open(chk[refname][i])
except IOError as e:
raise IOError('Unable to open {0} file: {1}'.format(
i, chk[refname][i]))
else:
fp.close()
# Set refname and assign the dictionary to the member
chk[refname]['refname'] = refname
self.assembly = chk[refname]
def _set_project_files(self):
'''Sets the project path, log, jobs, config, and results paths for the project.
project_path - parent directory for this project
config_path - parent directory for all config files within this project
job_path - parent directory for all job files within this project
log_path - parent directory for all log files within this project
results_path - parent directory for all results files within this project
report_path - parent directory for all report files within this project
'''
self.files = {
'project_path':
os.path.abspath(self.args.output_directory),
'config_path':
os.path.join(os.path.abspath(self.args.output_directory),
'config'),
'log_path':
os.path.join(os.path.abspath(self.args.output_directory), 'logs'),
'results_path':
os.path.join(os.path.abspath(self.args.output_directory),
'results'),
'report_path':
os.path.join(os.path.abspath(self.args.output_directory), 'report')
}
[check_dir(i) for i in self.files.values()]
def __write_bds_config(self):
'''Write the default BDS config file for an amazon cloud run'''
self.bds_file = os.path.join(
os.path.abspath(self.args.output_directory), 'bds.config')
with open(self.bds_file, 'wb') as o:
o.write('# BDS configuration file\n')
o.write(
'# This is set up to work easily with STAR cluster on EC2\n')
o.write(
'# Please see http://pcingola.github.io/BigDataScript/bigDataScript_manual.html#config\n'
)
o.write('# for more information.\n\n')
o.write('# Easy way to change mem usage for all jobs\n')
o.write('#mem = -1\n\n')
o.write('# Easy way to declare a particular node for all jobs\n')
o.write('#node = my_node\n\n')
o.write('# Easy way to declare a particular queue for all jobs\n')
o.write('#queue = my_queue\n\n')
o.write(
'# Easy way to declare the timeout for all jobs (seconds). It is 24 hours by default\n'
)
o.write('#timeout = 86400\n\n')
o.write(
'# Number of times a failed job can be retried. We find 0 is the safest.\n'
)
o.write('retry = 0\n\n')
o.write(
'# Sometimes many qsub commands is not able to be handled on some systems.\n'
)
o.write(
'# Use this to set the number of milliseconds to wait after qsub.\n'
)
o.write('waitAfterTaskRun = 200\n\n')
o.write('# Use bash shell for tasks\n')
o.write('taskShell = /bin/bash -e\n\n')
o.write('# SGE parallel environment\n')
o.write('sge.pe = smp\n\n')
o.write(
'# SGE mem argument. We set mem_free as consumable, jobs will wait, but it does not\n'
)
o.write(
'# guarantee that memory will be available (e.g., it will not kill jobs that use more\n'
)
o.write(
'# memory than requested. You can change memory usage for each tool in the ExScalibur configs\n'
)
o.write('sge.mem = mem_free\n\n')
o.write('# SGE timeout variable\n')
o.write('sge.timeout = h_rt\n\n')
def __write_project_run_script(self):
'''The script for running ExScalibur'''
bds_script = os.path.join(self.PATH, 'ExScaliburSMD-run.bds')
main_job = os.path.join(self.files['project_path'],
'{0.name}.exscalibur-smd.sh'.format(self))
bds_log = os.path.join(self.files['project_path'], 'BDS-System.logs')
cri_log = os.path.join(self.files['project_path'], 'CRI-Info.logs')
# Create the job script
with open(main_job, 'wb') as o:
o.write('#!/bin/bash\n')
o.write('\n')
o.write('cd {0}\n\n'.format(self.files['project_path']))
if self.settings.system['module_source']:
o.write('. {0}\n'.format(
self.settings.system['module_source']))
if self.settings.system['java']['use_module']:
o.write('module load {0}\n\n'.format(
self.settings.system['java']['module']['name']))
o.write('# Command for running the ExScalibur-SMD pipeline\n\n')
o.write('bds -c ' + self.bds_file + ' -reportHtml -reportYaml -v -log -s sge ' + \
'{0} -in {1} -options {2} > {3} 2> {4}\n'.format(
bds_script, " ".join(self.config_list), self.settings.settings_cfg,
cri_log, bds_log))
# Make user executable
import stat
st = os.stat(main_job)
os.chmod(main_job, st.st_mode | stat.S_IEXEC)
###################################
## Reporter functions
def __write_reporter_yaml(self):
'''Writes the pipeline reporter yaml file'''
self.final_reporter_yaml = os.path.join(
self.files['report_path'],
'{0.name}.exscalibur.smd.yaml'.format(self))
dic = {'data': [], 'project': self.name}
for s in self.samples:
curr = s.reporter_obj
dic['data'].append({
'fastqc': self.__reporter_fastqc(curr),
'alignments': self.__reporter_alignments(curr),
'somatic': self.__reporter_somatic(curr),
'sample': s.name
})
with open(self.final_reporter_yaml, 'wb') as o:
yaml.safe_dump(dic, o)
def __reporter_fastqc(self, dic):
'''Creates the relative paths for fastqc files'''
normal = dic['reads']['outputs']['normal']
curr_normal = [{
'readgroup':
i['readgroup'],
'leftseq':
os.path.relpath(i['leftseq'], start=self.files['report_path']),
'rightseq':
os.path.relpath(i['rightseq'], start=self.files['report_path'])
if i['paired'] else None,
'paired':
i['paired']
} for i in normal]
tumor = dic['reads']['outputs']['tumor']
curr_tumor = [{
'readgroup':
i['readgroup'],
'leftseq':
os.path.relpath(i['leftseq'], start=self.files['report_path']),
'rightseq':
os.path.relpath(i['rightseq'], start=self.files['report_path'])
if i['paired'] else None,
'paired':
i['paired']
} for i in tumor]
return {'inputs': {'normal': curr_normal, 'tumor': curr_tumor}}
def __reporter_alignments(self, dic):
'''Creates the relative paths for the alignment files'''
curr = dic['alignments']['outputs']
return {
'inputs': {
'alignment_summary_metrics':
os.path.relpath(curr['alignment_summary_metrics'],
start=self.files['report_path']),
'insert_size_metrics':
os.path.relpath(curr['insert_size_metrics'],
start=self.files['report_path']),
'total_coverage':
os.path.relpath(curr['total_coverage'],
start=self.files['report_path'])
}
}
def __reporter_somatic(self, dic):
'''Creates the relative paths for the somatic files'''
return {
'inputs': {
'somatic_table':
os.path.relpath(dic['somatic']['outputs']['smd_snp_table'],
start=self.files['report_path'])
}
}
class Project(object):
"""Object representing a Tumor/Normal Exome Project
-- args - the argparser object
-- PATH - the path to the ExScaliburSMD application directory
-- assembly - the assembly dictionary from the assembly yaml file
-- settings - the PipelineSettings object
-- files - dictionary of main project paths
-- samples - the SampleFactory object
-- name - the project ID
"""
def __init__(self, args, PATH):
self.logger = logging.getLogger("SMD.Project")
self.args = args
self.PATH = PATH
self.assembly = None
self.settings = None
self.files = None
self.name = args.project_id
self.samples = SampleFactory()
self.final_reporter_yaml = None
self.bds_file = None
# Lists holding the job submission commands to write to the
# submission scripts
self.preprocessing_jobs = []
self.alignments_jobs = []
self.gatk_jobs = []
self.somatic_jobs = []
self.annotation_jobs = []
self.report_jobs = []
self.config_list = []
def initialize_project(self):
"""Wrapper for building the project.
1. Load the settings
2. Load the assembly
3. Load the samples
4. Set the directory structure
"""
self.logger.info("Project Name: {0.name}".format(self))
# Settings
self.settings = PipelineSettings(self.args, self.PATH)
self.logger.info("Baseline Threads: {0.threads}".format(self.settings))
self.logger.info("Clip Adapters: {0.clipping}".format(self.settings))
if self.settings.clipping:
self.logger.info("Minimum read length: {0.min_length}".format(self.settings))
self.logger.info("Minimum MAPQ: {0.min_map_q}".format(self.settings))
self.logger.info("Aligners: {0}".format(self.settings.aln_list))
self.logger.info("Somatic Mutation Detectors: {0}".format(self.settings.smd_list))
# Assembly info
self._set_assembly()
self.logger.info("Reference Name: {0}".format(self.assembly["refname"]))
# Samples
self.samples.load_samples(os.path.abspath(self.args.metadata), self.PATH, self.name)
# File structure
self._set_project_files()
def configure_pipeline(self):
"""Wrapper for creating the configuration files for each sample"""
self.settings.write_settings_cfg(self)
for s in self.samples:
s.write_sample_bds(self, self.settings)
s.write_sample_report_yaml()
self.config_list.append(s.sample_cfg)
self.__write_reporter_yaml()
self.__write_bds_config()
self.__write_project_run_script()
def _set_assembly(self):
"""Grabs the yaml file, validates it, and returns the dictionary"""
# Load
in_fh = open(self.args.config_file, "rU")
chk = yaml.safe_load(in_fh)["reference"]
in_fh.close()
# Check the file
refname = chk.keys()[0]
required = ["cosmic", "exons_bed", "knowndb", "knownindel", "referenceseq", "sequence_dictionary"]
if "novoalign" in self.settings.aln_list:
required.append("novoalign_index")
for i in required:
assert i in chk[refname], self.logger.error("Required refrence section '%s' missing" % i)
if i in ["cosmic", "exons_bed", "knowndb", "knownindel", "referenceseq", "sequence_dictionary"]:
try:
fp = open(chk[refname][i])
except IOError as e:
raise IOError("Unable to open {0} file: {1}".format(i, chk[refname][i]))
else:
fp.close()
# Set refname and assign the dictionary to the member
chk[refname]["refname"] = refname
self.assembly = chk[refname]
def _set_project_files(self):
"""Sets the project path, log, jobs, config, and results paths for the project.
project_path - parent directory for this project
config_path - parent directory for all config files within this project
job_path - parent directory for all job files within this project
log_path - parent directory for all log files within this project
results_path - parent directory for all results files within this project
report_path - parent directory for all report files within this project
"""
self.files = {
"project_path": os.path.abspath(self.args.output_directory),
"config_path": os.path.join(os.path.abspath(self.args.output_directory), "config"),
"log_path": os.path.join(os.path.abspath(self.args.output_directory), "logs"),
"results_path": os.path.join(os.path.abspath(self.args.output_directory), "results"),
"report_path": os.path.join(os.path.abspath(self.args.output_directory), "report"),
}
[check_dir(i) for i in self.files.values()]
def __write_bds_config(self):
"""Write the default BDS config file for an amazon cloud run"""
self.bds_file = os.path.join(os.path.abspath(self.args.output_directory), "bds.config")
with open(self.bds_file, "wb") as o:
o.write("# BDS configuration file\n")
o.write("# This is set up to work easily with STAR cluster on EC2\n")
o.write("# Please see http://pcingola.github.io/BigDataScript/bigDataScript_manual.html#config\n")
o.write("# for more information.\n\n")
o.write("# Easy way to change mem usage for all jobs\n")
o.write("#mem = -1\n\n")
o.write("# Easy way to declare a particular node for all jobs\n")
o.write("#node = my_node\n\n")
o.write("# Easy way to declare a particular queue for all jobs\n")
o.write("#queue = my_queue\n\n")
o.write("# Easy way to declare the timeout for all jobs (seconds). It is 24 hours by default\n")
o.write("#timeout = 86400\n\n")
o.write("# Number of times a failed job can be retried. We find 0 is the safest.\n")
o.write("retry = 0\n\n")
o.write("# Sometimes many qsub commands is not able to be handled on some systems.\n")
o.write("# Use this to set the number of milliseconds to wait after qsub.\n")
o.write("waitAfterTaskRun = 200\n\n")
o.write("# Use bash shell for tasks\n")
o.write("taskShell = /bin/bash -e\n\n")
o.write("# SGE parallel environment\n")
o.write("sge.pe = smp\n\n")
o.write("# SGE mem argument. We set mem_free as consumable, jobs will wait, but it does not\n")
o.write("# guarantee that memory will be available (e.g., it will not kill jobs that use more\n")
o.write("# memory than requested. You can change memory usage for each tool in the ExScalibur configs\n")
o.write("sge.mem = mem_free\n\n")
o.write("# SGE timeout variable\n")
o.write("sge.timeout = h_rt\n\n")
def __write_project_run_script(self):
"""The script for running ExScalibur"""
bds_script = os.path.join(self.PATH, "ExScaliburSMD-run.bds")
main_job = os.path.join(self.files["project_path"], "{0.name}.exscalibur-smd.sh".format(self))
bds_log = os.path.join(self.files["project_path"], "BDS-System.logs")
cri_log = os.path.join(self.files["project_path"], "CRI-Info.logs")
# Create the job script
with open(main_job, "wb") as o:
o.write("#!/bin/bash\n")
o.write("\n")
o.write("cd {0}\n\n".format(self.files["project_path"]))
if self.settings.system["module_source"]:
o.write(". {0}\n".format(self.settings.system["module_source"]))
if self.settings.system["java"]["use_module"]:
o.write("module load {0}\n\n".format(self.settings.system["java"]["module"]["name"]))
o.write("# Command for running the ExScalibur-SMD pipeline\n\n")
o.write(
"bds -c "
+ self.bds_file
+ " -reportHtml -reportYaml -v -log -s sge "
+ "{0} -in {1} -options {2} > {3} 2> {4}\n".format(
bds_script, " ".join(self.config_list), self.settings.settings_cfg, cri_log, bds_log
)
)
# Make user executable
import stat
st = os.stat(main_job)
os.chmod(main_job, st.st_mode | stat.S_IEXEC)
###################################
## Reporter functions
def __write_reporter_yaml(self):
"""Writes the pipeline reporter yaml file"""
self.final_reporter_yaml = os.path.join(self.files["report_path"], "{0.name}.exscalibur.smd.yaml".format(self))
dic = {"data": [], "project": self.name}
for s in self.samples:
curr = s.reporter_obj
dic["data"].append(
{
"fastqc": self.__reporter_fastqc(curr),
"alignments": self.__reporter_alignments(curr),
"somatic": self.__reporter_somatic(curr),
"sample": s.name,
}
)
with open(self.final_reporter_yaml, "wb") as o:
yaml.safe_dump(dic, o)
def __reporter_fastqc(self, dic):
"""Creates the relative paths for fastqc files"""
normal = dic["reads"]["outputs"]["normal"]
curr_normal = [
{
"readgroup": i["readgroup"],
"leftseq": os.path.relpath(i["leftseq"], start=self.files["report_path"]),
"rightseq": os.path.relpath(i["rightseq"], start=self.files["report_path"]) if i["paired"] else None,
"paired": i["paired"],
}
for i in normal
]
tumor = dic["reads"]["outputs"]["tumor"]
curr_tumor = [
{
"readgroup": i["readgroup"],
"leftseq": os.path.relpath(i["leftseq"], start=self.files["report_path"]),
"rightseq": os.path.relpath(i["rightseq"], start=self.files["report_path"]) if i["paired"] else None,
"paired": i["paired"],
}
for i in tumor
]
return {"inputs": {"normal": curr_normal, "tumor": curr_tumor}}
def __reporter_alignments(self, dic):
"""Creates the relative paths for the alignment files"""
curr = dic["alignments"]["outputs"]
return {
"inputs": {
"alignment_summary_metrics": os.path.relpath(
curr["alignment_summary_metrics"], start=self.files["report_path"]
),
"insert_size_metrics": os.path.relpath(curr["insert_size_metrics"], start=self.files["report_path"]),
"total_coverage": os.path.relpath(curr["total_coverage"], start=self.files["report_path"]),
}
}
def __reporter_somatic(self, dic):
"""Creates the relative paths for the somatic files"""
return {
"inputs": {
"somatic_table": os.path.relpath(
dic["somatic"]["outputs"]["smd_snp_table"], start=self.files["report_path"]
)
}
}
