def collectRptScout(DIR, tool):
# FIRST: Get any applicable RM output stats
for org in data_map.keys():
for f in f_list:
RS_job_file = DIR + "/../job_log/{prefix}.{org}.s0.f{f}".format(prefix=tool_prefix[tool], org=org, f=f)
RM_job_file = DIR + "/../job_log/rm.{prefix}.{org}.s0.f{f}".format(prefix=tool_prefix[tool], org=org, f=f)
RS_dir = DIR + "/" + ("{org}.s0.f{f}".format(org=org, f=f)).upper()
RM_file = RS_dir + "/" + "{org}.fa.out".format(org=org, f=f)
blast_file = RS_dir + "/" + "{org}.s0.f{f}.RS.blast.6.txt.bz2".format(org=org, f=f)
pra_output = "{DIR}/{org}.s0.f{f}.pra.txt".format(DIR=RS_dir, org=org, f=f)
tool_output = RM_file
real_repeats = data_map[org] + ".out"
H = create_stats_hash(tool, org, None, int(f))
# Get stats from RM run
try:
Counts, Stats, Sets = perform_stats.perform_stats(real_repeats, tool_output, None)
H["tp"], H["fp"], H["fn"], H["tn"] = Counts
H["tpr"], H["tnr"], H["ppv"], H["npv"], H["fpr"], H["fdr"] = Stats
except Exception as E:
pass
# raise E;
# Get resource usage from RPT_SCOUT run
if os.path.exists(RS_job_file):
p = redhawk.loadPBS(open(RS_job_file, "rb"))[0]
try:
if p.efile_exists():
H["ToolCpuTime"], H["ToolWallTime"], H["ToolMem"], H["ToolVMem"] = p.getResources()
except:
pass
redhawk.storePBS([p], open(RS_job_file, "wb"))
# Get resource usage from RM run
if os.path.exists(RM_job_file):
p = redhawk.loadPBS(open(RM_job_file, "rb"))[0]
try:
if p.efile_exists():
H["RMCpuTime"], H["RMWallTime"], H["RMMem"], H["RMVMem"] = p.getResources()
except:
pass
redhawk.storePBS([p], open(RM_job_file, "wb"))
if os.path.exists(blast_file):
cmd = "bzcat {blast_output} | ./pra_analysis2 {output}".format(
blast_output=blast_file, output=pra_output
)
subprocess.call(cmd, shell=True)
query_cover, target_cover, Used = parse_pra_output.parse_pra_output(pra_output, "exclude.txt")
H["ConCoverage"], H["QuCoverage"] = query_cover, target_cover
stats_map[(tool, org, None, f)] = H
return None
def collectRaider(DIR, tool):
# FIRST: Get any applicable RM output stats
for org in data_map.keys():
for seed_num in seed_map.keys():
for f in f_list:
print("File: " + org + " " + str(seed_num) + " " + str(f) + "\n")
RAIDER_job_file = DIR + "/../job_log/{prefix}.{org}.s{seed_num}.f{f}".format(
prefix=tool_prefix[tool], org=org, seed_num=seed_num, f=f
)
RM_job_file = DIR + "/../job_log/rm.{prefix}.{org}.s{seed_num}.f{f}".format(
prefix=tool_prefix[tool], org=org, seed_num=seed_num, f=f
)
RM_dir = DIR + "/" + ("{org}.s{seed}.f{f}".format(org=org, seed=seed_num, f=f)).upper()
RM_file = RM_dir + "/" + "{org}.fa.out".format(org=org, seed=seed_num, f=f)
blast_file = RM_dir + "/" + "{org}.s{seed}.f{f}.blast.6.txt.bz2".format(org=org, seed=seed_num, f=f)
pra_output = RM_dir + "/" + "{org}.s{seed}.f{f}.pra.txt".format(org=org, seed=seed_num, f=f)
tool_output = RM_file
real_repeats = data_map[org] + ".out"
H = create_stats_hash(tool, org, int(seed_num), int(f))
seed = convert_seed(seed_map[seed_num])
seed_len = len(seed)
seed_weight = seed.count("1")
seed_ratio = seed_weight / (float(seed_len))
H["l"] = seed_len
H["w"] = seed_weight
H["w/l"] = seed_ratio
# Get stats from RM run
try:
Counts, Stats, Sets = perform_stats.perform_stats(real_repeats, tool_output, None)
H["tp"], H["fp"], H["fn"], H["tn"] = Counts
H["tpr"], H["tnr"], H["ppv"], H["npv"], H["fpr"], H["fdr"] = Stats
except Exception as E:
pass
# raise E;
# Get resource usage from RAIDER run
if os.path.exists(RAIDER_job_file):
p = redhawk.loadPBS(open(RAIDER_job_file, "rb"))[0]
try:
if p.efile_exists():
H["ToolCpuTime"], H["ToolWallTime"], H["ToolMem"], H["ToolVMem"] = p.getResources()
except:
pass
redhawk.storePBS([p], open(RAIDER_job_file, "wb"))
# Get resource usage from RM run
if os.path.exists(RM_job_file):
p = redhawk.loadPBS(open(RM_job_file, "rb"))[0]
try:
if p.efile_exists():
H["RMCpuTime"], H["RMWallTime"], H["RMMem"], H["RMVMem"] = p.getResources()
except:
pass
redhawk.storePBS([p], open(RM_job_file, "wb"))
if os.path.exists(blast_file):
if not os.path.exists(pra_output):
cmd = "bzcat {blast_output} | ./pra_analysis2 {output}".format(
blast_output=blast_file, output=pra_output
)
print("cmd: " + cmd)
# subprocess.call(cmd, shell=True)
query_cover, target_cover, Used = parse_pra_output.parse_pra_output(pra_output, "exclude.txt")
H["ConCoverage"], H["QuCoverage"] = query_cover, target_cover
stats_map[(tool, org, seed_num, f)] = H
return None
def collectRaider(DIR, tool):
# FIRST: Get any applicable RM output stats
for org in data_map.keys():
for seed_num in seed_map.keys():
for f in f_list:
print("File: " + org + " " + str(seed_num) + " " + str(f))
RAIDER_job_file = DIR + "/../job_log/{prefix}.{org}.s{seed_num}.f{f}".format(prefix = tool_prefix[tool], org=org, seed_num=seed_num, f=f)
RM_job_file = DIR + "/../job_log/rm.{prefix}.{org}.s{seed_num}.f{f}".format(prefix = tool_prefix[tool], org=org, seed_num=seed_num, f=f)
RM_dir = DIR + "/" + ("{org}.s{seed}.f{f}".format(org=org, seed=seed_num, f=f)).upper()
RM_file = RM_dir + "/" + "{org}.fa.out".format(org=org, seed=seed_num, f=f)
blast_file = RM_dir + "/" + "{org}.s{seed}.f{f}.blast.6.txt.bz2".format(org=org, seed=seed_num, f=f)
pra_output = RM_dir + "/" + "{org}.s{seed}.f{f}.pra.txt".format(org=org, seed=seed_num, f=f)
tool_output = RM_file
real_repeats = data_map[org] + ".out"
H = create_stats_hash(tool, org, int(seed_num), int(f))
seed = convert_seed(seed_map[seed_num])
seed_len = len(seed)
seed_weight = seed.count("1")
seed_ratio = seed_weight / (float(seed_len))
H['l'] = seed_len
H['w'] = seed_weight
H['w/l'] = seed_ratio
# Get stats from RM run
try:
negatives, fp, fp_d, positives, tp, famHash = rm_analysis.collect_stats(real_repeats, tool_output, fp_dist)
H['tp'] = tp
H['fp'] = fp # DEBUG: NEED TO DOUBLE-CHECK THIS!!!
H['tn'] = negatives - H['fp']
H['fn'] = positives - H['tp']
H['tpr'] = H['tp'] / positives
H['tnr'] = H['tn'] / negatives
H['ppv'] = H['tp'] / (H['tp'] + H['fp'])
H['npv'] = H['tn'] / (H['tn'] + H['fn'])
H['fpr'] = H['fp'] / negatives
H['fnr'] = 1 - H['tpr']
H['dfr'] = 1 - H['ppv']
#Counts, Stats, Sets = perform_stats.perform_stats(real_repeats, tool_output, None)
#H['tp'], H['fp'], H['fn'], H['tn'] = Counts
#H['tpr'], H['tnr'], H['ppv'], H['npv'], H['fpr'], H['fdr'] = Stats
except Exception as E:
#raise E;
pass
# Get resource usage from RAIDER run
if os.path.exists(RAIDER_job_file):
p = redhawk.loadPBS(open(RAIDER_job_file, "rb"))[0]
try:
if p.efile_exists():
H['ToolCpuTime'], H['ToolWallTime'], H['ToolMem'], H['ToolVMem'] = p.getResources()
except:
pass
redhawk.storePBS([p], open(RAIDER_job_file, "wb"))
# Get resource usage from RM run
if os.path.exists(RM_job_file):
p = redhawk.loadPBS(open(RM_job_file, "rb"))[0]
try:
if p.efile_exists():
H['RMCpuTime'], H['RMWallTime'], H['RMMem'], H['RMVMem'] = p.getResources()
except:
pass
redhawk.storePBS([p], open(RM_job_file, "wb"))
#print("BF: " + blast_file)
#print("PRA: " + pra_output)
if os.path.exists(blast_file):
if not os.path.exists(pra_output):
cmd = "bzcat {blast_output} | ./pra_analysis2 {output}".format(blast_output=blast_file, output=pra_output)
#print("cmd: " + cmd)
subprocess.call(cmd, shell=True)
query_cover, target_cover, Used = parse_pra_output.parse_pra_output(pra_output, "exclude.txt")
H['ConCoverage'], H['QuCoverage'] = query_cover, target_cover
stats_map[(tool,org,seed_num,f)] = H
return None
def collectRptScout(DIR, tool):
# FIRST: Get any applicable RM output stats
for org in data_map.keys():
for f in f_list:
RS_job_file = DIR + "/../job_log/{prefix}.{org}.s0.f{f}".format(prefix = tool_prefix[tool], org=org, f=f)
RM_job_file = DIR + "/../job_log/rm.{prefix}.{org}.s0.f{f}".format(prefix = tool_prefix[tool], org=org, f=f)
RS_dir = DIR + "/" + ("{org}.s0.f{f}".format(org=org, f=f)).upper()
RM_file = RS_dir + "/" + "{org}.fa.out".format(org=org, f=f)
blast_file = RS_dir + "/" + "{org}.s0.f{f}.RS.blast.6.txt.bz2".format(org=org, f=f)
pra_output = "{DIR}/{org}.s0.f{f}.pra.txt".format(DIR=RS_dir, org=org, f=f)
tool_output = RM_file
real_repeats = data_map[org] + ".out"
H = create_stats_hash(tool, org, None, int(f))
# Get stats from RM run
try:
negatives, fp, fp_d, positives, tp, famHash = rm_analysis.collect_stats(real_repeats, tool_output, fp_dist)
H['tp'] = tp
H['fp'] = fp # DEBUG: NEED TO DOUBLE-CHECK THIS!!!
H['tn'] = negatives - H['fp']
H['fn'] = positives - H['tp']
H['tpr'] = H['tp'] / positives
#print(H['tpr'])
H['tnr'] = H['tn'] / negatives
H['ppv'] = H['tp'] / (H['tp'] + H['fp'])
H['npv'] = H['tn'] / (H['tn'] + H['fn'])
H['fpr'] = H['fp'] / negatives
H['fnr'] = 1 - H['tpr']
H['dfr'] = 1 - H['ppv']
#Counts, Stats, Sets = perform_stats.perform_stats(real_repeats, tool_output, None)
#H['tp'], H['fp'], H['fn'], H['tn'] = Counts
#H['tpr'], H['tnr'], H['ppv'], H['npv'], H['fpr'], H['fdr'] = Stats
except Exception as E:
pass
#raise E;
# Get resource usage from RPT_SCOUT run
if os.path.exists(RS_job_file):
p = redhawk.loadPBS(open(RS_job_file, "rb"))[0]
try:
if p.efile_exists():
H['ToolCpuTime'], H['ToolWallTime'], H['ToolMem'], H['ToolVMem'] = p.getResources()
except:
pass
redhawk.storePBS([p], open(RS_job_file, "wb"))
# Get resource usage from RM run
if os.path.exists(RM_job_file):
p = redhawk.loadPBS(open(RM_job_file, "rb"))[0]
try:
if p.efile_exists():
H['RMCpuTime'], H['RMWallTime'], H['RMMem'], H['RMVMem'] = p.getResources()
except:
pass
redhawk.storePBS([p], open(RM_job_file, "wb"))
if os.path.exists(blast_file):
cmd = "bzcat {blast_output} | ./pra_analysis2 {output}".format(blast_output=blast_file, output=pra_output)
subprocess.call(cmd, shell=True)
query_cover, target_cover, Used = parse_pra_output.parse_pra_output(pra_output, "exclude.txt")
H['ConCoverage'], H['QuCoverage'] = query_cover, target_cover
stats_map[(tool,org,None,f)] = H
return None
def collectRptScout(DIR, tool):
# FIRST: Get any applicable RM output stats
for org in data_map.keys():
for f in f_list:
RS_job_file = DIR + "/../job_log/{prefix}.{org}.s0.f{f}".format(
prefix=tool_prefix[tool], org=org, f=f)
RM_job_file = DIR + "/../job_log/rm.{prefix}.{org}.s0.f{f}".format(
prefix=tool_prefix[tool], org=org, f=f)
RS_dir = DIR + "/" + ("{org}.s0.f{f}".format(org=org, f=f)).upper()
RM_file = RS_dir + "/" + "{org}.fa.out".format(org=org, f=f)
blast_file = RS_dir + "/" + "{org}.s0.f{f}.RS.blast.6.txt.bz2".format(
org=org, f=f)
pra_output = "{DIR}/{org}.s0.f{f}.pra.txt".format(DIR=RS_dir,
org=org,
f=f)
tool_output = RM_file
real_repeats = data_map[org] + ".out"
H = create_stats_hash(tool, org, None, int(f))
# Get stats from RM run
try:
negatives, fp, fp_d, positives, tp, famHash = rm_analysis.collect_stats(
real_repeats, tool_output, fp_dist)
H['tp'] = tp
H['fp'] = fp # DEBUG: NEED TO DOUBLE-CHECK THIS!!!
H['tn'] = negatives - H['fp']
H['fn'] = positives - H['tp']
H['tpr'] = H['tp'] / positives
#print(H['tpr'])
H['tnr'] = H['tn'] / negatives
H['ppv'] = H['tp'] / (H['tp'] + H['fp'])
H['npv'] = H['tn'] / (H['tn'] + H['fn'])
H['fpr'] = H['fp'] / negatives
H['fnr'] = 1 - H['tpr']
H['dfr'] = 1 - H['ppv']
#Counts, Stats, Sets = perform_stats.perform_stats(real_repeats, tool_output, None)
#H['tp'], H['fp'], H['fn'], H['tn'] = Counts
#H['tpr'], H['tnr'], H['ppv'], H['npv'], H['fpr'], H['fdr'] = Stats
except Exception as E:
pass
#raise E;
# Get resource usage from RPT_SCOUT run
if os.path.exists(RS_job_file):
p = redhawk.loadPBS(open(RS_job_file, "rb"))[0]
try:
if p.efile_exists():
H['ToolCpuTime'], H['ToolWallTime'], H['ToolMem'], H[
'ToolVMem'] = p.getResources()
except:
pass
redhawk.storePBS([p], open(RS_job_file, "wb"))
# Get resource usage from RM run
if os.path.exists(RM_job_file):
p = redhawk.loadPBS(open(RM_job_file, "rb"))[0]
try:
if p.efile_exists():
H['RMCpuTime'], H['RMWallTime'], H['RMMem'], H[
'RMVMem'] = p.getResources()
except:
pass
redhawk.storePBS([p], open(RM_job_file, "wb"))
if os.path.exists(blast_file):
cmd = "bzcat {blast_output} | ./pra_analysis2 {output}".format(
blast_output=blast_file, output=pra_output)
subprocess.call(cmd, shell=True)
query_cover, target_cover, Used = parse_pra_output.parse_pra_output(
pra_output, "exclude.txt")
H['ConCoverage'], H['QuCoverage'] = query_cover, target_cover
stats_map[(tool, org, None, f)] = H
return None
def collectNaive(DIR, tool): # NAIVE
# FIRST: Get any applicable RM output stats
assert (tool == 'naive')
for org in data_map.keys():
for seed_num in seed_map.keys():
for f in f_list:
print("File: " + org + " " + str(seed_num) + " " + str(f))
NAIVE_job_file = DIR + "/../job_log/{prefix}.{org}.s{seed_num}.f{f}".format(
prefix=tool_prefix[tool], org=org, seed_num=seed_num, f=f)
RM_job_file = DIR + "/../job_log/rm.{prefix}.{org}.s{seed_num}.f{f}".format(
prefix=tool_prefix[tool], org=org, seed_num=seed_num, f=f)
RM_dir = DIR + "/" + ("{org}.s{seed}.f{f}".format(
org=org, seed=seed_num, f=f)).upper()
RM_file = RM_dir + "/" + "{org}.fa.out".format(
org=org, seed=seed_num, f=f)
blast_file = RM_dir + "/" + "{org}.s{seed}.f{f}.blast.6.txt.bz2".format(
org=org, seed=seed_num, f=f)
pra_output = RM_dir + "/" + "{org}.s{seed}.f{f}.pra.txt".format(
org=org, seed=seed_num, f=f)
tool_output = RM_file
real_repeats = data_map[org] + ".out"
H = create_stats_hash(tool, org, int(seed_num), int(f))
seed = convert_seed(seed_map[seed_num])
seed_len = len(seed)
seed_weight = seed.count("1")
seed_ratio = seed_weight / (float(seed_len))
H['l'] = seed_len
H['w'] = seed_weight
H['w/l'] = seed_ratio
# Get stats from RM run
try:
negatives, fp, fp_d, positives, tp, famHash = rm_analysis.collect_stats(
real_repeats, tool_output, fp_dist)
H['tp'] = tp
H['fp'] = fp # DEBUG: NEED TO DOUBLE-CHECK THIS!!!
H['tn'] = negatives - H['fp']
H['fn'] = positives - H['tp']
H['tpr'] = H['tp'] / positives
#print(H['tpr'])
H['tnr'] = H['tn'] / negatives
H['ppv'] = H['tp'] / (H['tp'] + H['fp'])
H['npv'] = H['tn'] / (H['tn'] + H['fn'])
H['fpr'] = H['fp'] / negatives
H['fnr'] = 1 - H['tpr']
H['dfr'] = 1 - H['ppv']
#Counts, Stats, Sets = perform_stats.perform_stats(real_repeats, tool_output, None)
#H['tp'], H['fp'], H['fn'], H['tn'] = Counts
#H['tpr'], H['tnr'], H['ppv'], H['npv'], H['fpr'], H['fdr'] = Stats
except Exception as E:
pass
#raise E;
# Get resource usage from NAIVE run
if os.path.exists(NAIVE_job_file):
p = redhawk.loadPBS(open(NAIVE_job_file, "rb"))[0]
try:
if p.efile_exists():
H['ToolCpuTime'], H['ToolWallTime'], H[
'ToolMem'], H['ToolVMem'] = p.getResources()
except:
pass
redhawk.storePBS([p], open(NAIVE_job_file, "wb"))
# Get resource usage from RM run
if os.path.exists(RM_job_file):
p = redhawk.loadPBS(open(RM_job_file, "rb"))[0]
try:
if p.efile_exists():
H['RMCpuTime'], H['RMWallTime'], H['RMMem'], H[
'RMVMem'] = p.getResources()
except:
pass
redhawk.storePBS([p], open(RM_job_file, "wb"))
if os.path.exists(blast_file):
if not os.path.exists(pra_output):
cmd = "bzcat {blast_output} | ./pra_analysis2 {output}".format(
blast_output=blast_file, output=pra_output)
#print("cmd: " + cmd)
subprocess.call(cmd, shell=True)
query_cover, target_cover, Used = parse_pra_output.parse_pra_output(
pra_output, "exclude.txt")
H['ConCoverage'], H[
'QuCoverage'] = query_cover, target_cover
stats_map[(tool, org, seed_num, f)] = H
return None