def run(hg19Ref):
getData()
bam = "svviz-examples/chromEnds/begin.chr18.bam"
command = "svviz -t del -b {bam} {ref} chr18 30 9500 --no-web".format(ref=hg19Ref, bam=bam)
app.run(command.split())
bam = "svviz-examples/chromEnds/end.chr18.bam"
command = "svviz -t del -b {bam} {ref} chr18 78001429 78127146 --no-web".format(ref=hg19Ref, bam=bam)
app.run(command.split())
return True, ""
def run(hg19Ref):
getData()
bam = "svviz-examples/chromEnds/begin.chr18.bam"
command = "svviz -t del -b {bam} {ref} chr18 30 9500 --no-web".format(
ref=hg19Ref, bam=bam)
app.run(command.split())
bam = "svviz-examples/chromEnds/end.chr18.bam"
command = "svviz -t del -b {bam} {ref} chr18 78001429 78127146 --no-web".format(
ref=hg19Ref, bam=bam)
app.run(command.split())
return True, ""
def run():
commands = [
"svviz demo 1 -a --no-web", "svviz demo 2 -a --no-web",
"svviz demo 2 -a --no-web --auto-export", "svviz demo 3 -a --no-web"
]
times = []
for command in commands:
t0 = time.time()
app.run(command.split(" "))
times.append(time.time() - t0)
print(pandas.DataFrame({"command": commands, "time (s)": times}))
return (True, "")
def run():
commands = ["svviz demo 1 -a --no-web",
"svviz demo 2 -a --no-web",
"svviz demo 2 -a --no-web --auto-export",
"svviz demo 3 -a --no-web"]
times = []
for command in commands:
t0 = time.time()
app.run(command.split(" "))
times.append(time.time() - t0)
print pandas.DataFrame({"command":commands, "time (s)":times})
return (True, "")
def run(genome, vcfs, bams, previousSummaryPath):
timings = {}
summaries = pandas.DataFrame()
totalTime = 0
for vcf in vcfs:
name = os.path.basename(vcf)
print(">", name, "<")
args = []
args.append("test_script")
args.append("-t batch")
args.append("--pair-min-mapq 50")
args.append(" ".join("-b {}".format(bam) for bam in bams))
args.append(genome)
args.append(vcf)
args = " ".join(args).split()
print(args)
t0 = time.time()
curSummary = app.run(args)
t1 = time.time()
timings[name] = t1 - t0
totalTime += t1 - t0
curSummary = pandas.read_table(StringIO(six.text_type(curSummary)))
summaries = pandas.concat([curSummary, summaries])
if not os.path.exists(previousSummaryPath) or "-f" in sys.argv:
print("=" * 30, "SAVING", "=" * 30)
summaries.to_csv(previousSummaryPath, sep="\t")
print(summaries)
return (True, "")
else:
print("=" * 30, "COMPARING", "=" * 30)
previousSummary = pandas.read_table(previousSummaryPath, index_col=0)
combined = pandas.merge(previousSummary,
summaries,
how="outer",
on=["variant", "sample", "allele", "key"],
suffixes=["_prev", "_new"])
combined = combined.set_index(["variant", "sample", "allele",
"key"]) #.fillna(0)
combined["diff"] = combined["value_new"] - combined["value_prev"]
diff = combined.loc[~numpy.isclose(combined["diff"], 0), "diff"]
if diff.shape[0] == 0:
print("--- same as previous run ---")
# return [True, "", totalTime]
return (True, "")
else:
print(combined.loc[diff.index])
return (False, "not equal to previous")
def run(genome, vcfs, bams, previousSummaryPath):
timings = {}
summaries = pandas.DataFrame()
totalTime = 0
for vcf in vcfs:
name = os.path.basename(vcf)
print ">", name, "<"
args = []
args.append("test_script")
args.append("-t batch")
args.append("--pair-min-mapq 50")
args.append(" ".join("-b {}".format(bam) for bam in bams))
args.append(genome)
args.append(vcf)
args = " ".join(args).split()
print args
t0 = time.time()
curSummary = app.run(args)
t1 = time.time()
timings[name] = t1-t0
totalTime += t1-t0
curSummary = pandas.read_table(StringIO(curSummary))
summaries = pandas.concat([curSummary, summaries])
if not os.path.exists(previousSummaryPath) or "-f" in sys.argv:
print "="*30, "SAVING", "="*30
summaries.to_csv(previousSummaryPath, sep="\t")
print summaries
return (True, "")
else:
print "="*30, "COMAPRING", "="*30
previousSummary = pandas.read_table(previousSummaryPath, index_col=0)
combined = pandas.merge(previousSummary, summaries, how="outer",
on=["variant", "sample","allele","key"],
suffixes=["_prev", "_new"])
combined = combined.set_index(["variant", "sample","allele","key"])#.fillna(0)
combined["diff"] = combined["value_new"] - combined["value_prev"]
diff = combined.loc[~numpy.isclose(combined["diff"], 0), "diff"]
if diff.shape[0] == 0:
print "--- same as previous run ---"
# return [True, "", totalTime]
return (True, "")
else:
print combined.loc[diff.index]
return (False, "not equal to previous")
curSummaryPath = summaryPath.format(name)
args = []
args.append("test_script")
args.append("-t batch")
args.append("--summary {}".format(curSummaryPath))
args.append(" ".join("-b {}".format(bam) for bam in bams))
args.append(genome)
args.append(vcf)
args = " ".join(args).split()
print args
t0 = time.time()
app.run(args)
t1 = time.time()
timings[name] = t1-t0
curSummary = pandas.read_table(curSummaryPath)
summaries = pandas.concat([curSummary, summaries])
previousSummaryPath = "/Users/nspies/Projects/svviz/tests/previousSummary.tsv"
if not os.path.exists(previousSummaryPath) or "-f" in sys.argv:
print "="*30, "SAVING", "="*30
summaries.to_csv(previousSummaryPath, sep="\t")
print summaries
else:
print "="*30, "COMAPRING", "="*30
curSummaryPath = summaryPath.format(name)
args = []
args.append("test_script")
args.append("-t batch")
args.append("--summary {}".format(curSummaryPath))
args.append(" ".join("-b {}".format(bam) for bam in bams))
args.append(genome)
args.append(vcf)
args = " ".join(args).split()
print args
t0 = time.time()
app.run(args)
t1 = time.time()
timings[name] = t1 - t0
curSummary = pandas.read_table(curSummaryPath)
summaries = pandas.concat([curSummary, summaries])
previousSummaryPath = "/Users/nspies/Projects/svviz/tests/previousSummary.tsv"
if not os.path.exists(previousSummaryPath) or "-f" in sys.argv:
print "=" * 30, "SAVING", "=" * 30
summaries.to_csv(previousSummaryPath, sep="\t")
print summaries
else:
print "=" * 30, "COMAPRING", "=" * 30
import pandas
import time
from svviz import app
commands = ["svviz demo 1 -a --no-web",
"svviz demo 2 -a --no-web",
"svviz demo 2 -a --no-web --auto-export"]
times = []
for command in commands:
t0 = time.time()
app.run(command.split(" "))
times.append(time.time() - t0)
print pandas.DataFrame({"command":commands, "time (s)":times})
import pandas
import time
from svviz import app
commands = [
"svviz demo 1 -a --no-web", "svviz demo 2 -a --no-web",
"svviz demo 2 -a --no-web --auto-export"
]
times = []
for command in commands:
t0 = time.time()
app.run(command.split(" "))
times.append(time.time() - t0)
print pandas.DataFrame({"command": commands, "time (s)": times})