def repair_task_list():
"""main gain and loss algorithm"""
(sentinel_path, results_path, haplotype_path, cancer_dir_path,
tmpbams_path, finalbams_path) = taskHelpers.GetProjectNamePathRunID()
inputs = []
outputs = []
prev_sentinels = []
prev_sentinels.append(
taskHelpers.CreateFileList('{0}_findroi.sentinel', 1, sentinel_path))
sentinels = taskHelpers.CreateFileList('{0}_repair.sentinel', 1,
sentinel_path)
inputs.append(
taskHelpers.CreateFileList('{0}.{1}.roi.sorted.bam', 88, tmpbams_path,
"gain"))
outputs.append(
taskHelpers.CreateFileList('{0}.{1}.repaired.bam', 88, tmpbams_path,
"gain"))
sample_ids = taskHelpers.CreateFileList('{0}', 1, '')
job_parameters = taskHelpers.CreateTaskList(inputs, sentinels, outputs,
sample_ids, prev_sentinels)
for job in job_parameters:
yield job
def find_roi_bam_task_list():
"""populates task inputs and outputs"""
(sentinel_path, results_path, haplotype_path, cancer_dir_path,
tmpbams_path, finalbams_path) = taskHelpers.GetProjectNamePathRunID()
inputs = []
outputs = []
prev_sentinels = []
split_path = "/".join([results_path, "splitbams"])
prev_sentinels.append(
taskHelpers.CreateFileList('{0}_sortn.sentinel', 1, sentinel_path))
sentinels = taskHelpers.CreateFileList('{0}_findroi.sentinel', 1,
sentinel_path)
inputs.append(
taskHelpers.CreateFileList('{0}.byname.bam', 22, split_path,
"extractROI"))
outputs.append(
taskHelpers.CreateFileList('{0}.{1}.roi.bam', 88, tmpbams_path,
"extractROI")
) # max number of outputs chr*events*haplotypes (8 for 2 chromosomes)
sample_ids = taskHelpers.CreateFileList('{0}', 1, '')
job_parameters = taskHelpers.CreateTaskList(inputs, sentinels, outputs,
sample_ids, prev_sentinels)
for job in job_parameters:
yield job
def complete_pipeline_gain_task_list():
(sentinel_path, results_path, haplotype_path, cancer_dir_path,
tmpbams_path, finalbams_path) = taskHelpers.GetProjectNamePathRunID()
inputs = []
outputs = []
prev_sentinels = []
prev_sentinels.append(
taskHelpers.CreateFileList('{0}_subsample_gain.sentinel', 1,
sentinel_path))
sentinels = taskHelpers.CreateFileList('{0}_sortmerge.sentinel', 1,
sentinel_path)
inputs.append(
taskHelpers.CreateFileList('{0}_{1}_{2}.bam', 88, finalbams_path,
"FINAL"))
outputs.append(
taskHelpers.CreateFileList(params.GetOutputFileName(), 1,
finalbams_path))
sample_ids = taskHelpers.CreateFileList('{0}', 1, '')
job_parameters = taskHelpers.CreateTaskList(inputs, sentinels, outputs,
sample_ids, prev_sentinels)
for job in job_parameters:
yield job
def subsample_loss_task_list():
(sentinel_path,results_path,haplotype_path,cancer_dir_path,tmpbams_path, finalbams_path) = taskHelpers.GetProjectNamePathRunID()
inputs = []
outputs = []
prev_sentinels = []
prev_sentinels.append(taskHelpers.CreateFileList(
'{0}_mutate_loss.sentinel', 1, sentinel_path))
sentinels = taskHelpers.CreateFileList(
'{0}_subsample_loss.sentinel', 1, sentinel_path)
inputs.append(taskHelpers.CreateFileList('{0}.{1}.mutated.merged.sorted.bam', 12, tmpbams_path, "loss"))
outputs.append(taskHelpers.CreateFileList(
'{0}{1}_GAIN.bam', 12, tmpbams_path, "loss"))
sample_ids = taskHelpers.CreateFileList('{0}', 1, '')
job_parameters = taskHelpers.CreateTaskList(inputs, sentinels, outputs,
sample_ids, prev_sentinels)
for job in job_parameters:
yield job
def sort_by_name_task_list():
"""populates task inputs and outputs"""
(sentinel_path,results_path,haplotype_path,cancer_dir_path,tmpbams_path, finalbams_path) = taskHelpers.GetProjectNamePathRunID()
inputs = []
outputs = []
prev_sentinels = []
split_path = "/".join([results_path, "splitbams"])
prev_sentinels.append(taskHelpers.CreateFileList(
'{0}_split.sentinel', 1, sentinel_path))
sentinels = taskHelpers.CreateFileList(
'{0}_sortn.sentinel', 1, sentinel_path)
inputs.append(taskHelpers.CreateFileList(
'chr{1}.bam', 3, split_path+"/"))
outputs.append(taskHelpers.CreateFileList(
'chr{1}.byname.bam', 3 ,split_path+"/"))
sample_ids = taskHelpers.CreateFileList('{0}', 1, '')
job_parameters = taskHelpers.CreateTaskList(inputs, sentinels, outputs,
sample_ids, prev_sentinels)
for job in job_parameters:
yield job
def split_bam_task_list():
"""populates task inputs and outputs"""
(sentinel_path, results_path, haplotype_path, cancer_dir_path,
tmpbams_path, finalbams_path) = taskHelpers.GetProjectNamePathRunID()
inputs = []
outputs = []
prev_sentinels = []
prev_sentinels.append(taskHelpers.CreateFileList('None', -1,
sentinel_path))
split_path = "/".join([results_path, "splitbams"])
params.SetSplitBamsPath(split_path)
utils.createDirectory(split_path)
sentinels = taskHelpers.CreateFileList('{0}_split.sentinel', 1,
sentinel_path)
inputs.append(taskHelpers.CreateFileList('bam', 1, split_path + "/"))
outputs.append(
taskHelpers.CreateFileList('chr{1}.bam', 22, split_path + "/"))
sample_ids = taskHelpers.CreateFileList('{0}', 1, '')
job_parameters = taskHelpers.CreateTaskList(inputs, sentinels, outputs,
sample_ids, prev_sentinels)
for job in job_parameters:
yield job