def runDirectExport(dataHub):
if dataHub.args.export:
logging.info("* Exporting views *")
ensureExportData(dataHub)
exportFormat = export.getExportFormat(dataHub.args)
if dataHub.args.type == "batch":
if not os.path.exists(dataHub.args.export):
os.makedirs(dataHub.args.export)
elif not os.path.isdir(dataHub.args.export):
logging.error("In batch mode, --export must be passed as a directory, not a file: '{}'".format(dataHub.args.export))
sys.exit(1)
path = os.path.join(dataHub.args.export, "{}.{}".format(dataHub.variant.shortName(), exportFormat))
else:
path = dataHub.args.export
exportData = dataHub.trackCompositor.render()
if exportFormat != "svg":
converter = export.getExportConverter(dataHub.args, exportFormat)
exportData = export.convertSVG(exportData, exportFormat, converter)
with open(path, "w") as outf:
outf.write(exportData)
if dataHub.args.open_exported:
utilities.launchFile(dataHub.args.export)
if dataHub.args.dotplots:
dotplotPath = os.path.splitext(path)[0] + ".dotplot.png"
with open(dotplotPath, "wb") as dotplotFile:
dotplotFile.write(dataHub.dotplots["ref vs ref"])
def runDirectExport(dataHub):
if dataHub.args.export:
logging.info("* Exporting views *")
ensureExportData(dataHub)
exportFormat = export.getExportFormat(dataHub.args)
if dataHub.args.type == "batch" or dataHub.args.format is not None:
if not os.path.exists(dataHub.args.export):
os.makedirs(dataHub.args.export)
path = os.path.join(dataHub.args.export, "{}.{}".format(dataHub.variant.shortName(), exportFormat))
else:
path = dataHub.args.export
exportData = dataHub.trackCompositor.render()
if exportFormat != "svg":
converter = export.getExportConverter(dataHub.args, exportFormat)
exportData = export.convertSVG(exportData, exportFormat, converter)
outf = open(path, "w")
outf.write(exportData)
outf.close()
if dataHub.args.open_exported:
utilities.launchFile(dataHub.args.export)
def runDirectExport(dataHub):
if dataHub.args.export:
logging.info("* Exporting views *")
ensureExportData(dataHub)
exportFormat = export.getExportFormat(dataHub.args)
if dataHub.args.type == "batch" or dataHub.args.format is not None:
if not os.path.exists(dataHub.args.export):
os.makedirs(dataHub.args.export)
path = os.path.join(
dataHub.args.export,
"{}.{}".format(dataHub.variant.shortName(), exportFormat))
else:
path = dataHub.args.export
exportData = dataHub.trackCompositor.render()
if exportFormat != "svg":
converter = export.getExportConverter(dataHub.args, exportFormat)
exportData = export.convertSVG(exportData, exportFormat, converter)
outf = open(path, "w")
outf.write(exportData)
outf.close()
if dataHub.args.open_exported:
utilities.launchFile(dataHub.args.export)
def runDirectExport(dataHub):
if dataHub.args.export:
logging.info("* Exporting views *")
ensureExportData(dataHub)
exportFormat = export.getExportFormat(dataHub.args)
if dataHub.args.type == "batch":
if not os.path.exists(dataHub.args.export):
os.makedirs(dataHub.args.export)
elif not os.path.isdir(dataHub.args.export):
logging.error("In batch mode, --export must be passed as a directory, not a file: '{}'".format(dataHub.args.export))
sys.exit(1)
path = os.path.join(dataHub.args.export, "{}.{}".format(dataHub.variant.shortName(), exportFormat))
else:
path = dataHub.args.export
exportData = dataHub.trackCompositor.render()
filemode = "w"
if exportFormat != "svg":
converter = export.getExportConverter(dataHub.args, exportFormat)
exportData = export.convertSVG(exportData, exportFormat, converter)
filemode = "wb"
with open(path, filemode) as outf:
outf.write(exportData)
if dataHub.args.open_exported:
utilities.launchFile(dataHub.args.export)
outbasepath = os.path.splitext(path)[0]
if dataHub.args.dotplots:
dotplotPath = outbasepath + ".dotplot.png"
with open(dotplotPath, "wb") as dotplotFile:
dotplotFile.write(dataHub.dotplots["ref vs ref"])
if dataHub.args.export_insert_sizes:
didExportISD = False
plotInsertSizeDistributions(dataHub)
for name, sample in dataHub.samples.items():
if sample.insertSizePlot is not None:
outpath = outbasepath + ".insertsizes.{}.png".format(name)
with open(outpath, "w") as isdfile:
isdfile.write(sample.insertSizePlot)
didExportISD = True
if not didExportISD:
print("** Failed to plot the insert size distributions; please make sure the **")
print("** rpy2 is installed, your input bam files have sufficient numbers of **")
print("** reads (> 50,000), and that the reads are paired-ended eg Illumina **")
print("** and not PacBio **")
def runDirectExport(dataHub):
if dataHub.args.export:
logging.info("* Exporting views *")
ensureExportData(dataHub)
exportFormat = export.getExportFormat(dataHub.args)
if dataHub.args.type == "batch":
if not os.path.exists(dataHub.args.export):
os.makedirs(dataHub.args.export)
elif not os.path.isdir(dataHub.args.export):
logging.error(
"In batch mode, --export must be passed as a directory, not a file: '{}'"
.format(dataHub.args.export))
sys.exit(1)
path = os.path.join(
dataHub.args.export,
"{}.{}".format(dataHub.variant.shortName(), exportFormat))
else:
path = dataHub.args.export
exportData = dataHub.trackCompositor.render()
filemode = "w"
if exportFormat != "svg":
converter = export.getExportConverter(dataHub.args, exportFormat)
exportData = export.convertSVG(exportData, exportFormat, converter)
filemode = "wb"
with open(path, filemode) as outf:
outf.write(exportData)
if dataHub.args.open_exported:
utilities.launchFile(dataHub.args.export)
outbasepath = os.path.splitext(path)[0]
if dataHub.args.dotplots:
dotplotPath = outbasepath + ".dotplot.png"
with open(dotplotPath, "wb") as dotplotFile:
dotplotFile.write(dataHub.dotplots["ref vs ref"])
if dataHub.args.export_insert_sizes:
didExportISD = False
plotInsertSizeDistributions(dataHub)
for name, sample in dataHub.samples.items():
if sample.insertSizePlot is not None:
outpath = outbasepath + ".insertsizes.{}.png".format(name)
with open(outpath, "w") as isdfile:
isdfile.write(sample.insertSizePlot)
didExportISD = True
if not didExportISD:
print(
"** Failed to plot the insert size distributions; please make sure the **"
)
print(
"** rpy2 is installed, your input bam files have sufficient numbers of **"
)
print(
"** reads (> 50,000), and that the reads are paired-ended eg Illumina **"
)
print(
"** and not PacBio **"
)
def run():
timings = {}
for testName in [
"mei", "inv", "ins_moleculo", "ins_pacbio", "del_chr1",
"translocation"
]:
print(">", testName, "<")
exportPath = "renderTests/export_{}_new.svg".format(testName)
originalPath = "renderTests/export_{}_original.svg".format(testName)
d = gzip.open("renderTests/{}.pickle.gz".format(testName), "rb")
try:
dataHub = pickle.load(d, encoding="latin1")
except TypeError:
dataHub = pickle.load(d)
dataHub.args = MockArgs()
dataHub.args.thicker_lines = False
dataHub.args.export = exportPath
dataHub.args.context = 0
t0 = time.time()
app.renderSamples(dataHub)
app.ensureExportData(dataHub)
app.runDirectExport(dataHub)
t1 = time.time()
timings[testName] = t1 - t0
no_changes = True
if not os.path.exists(originalPath):
print(" first time running; nothing to compare against")
shutil.copy(exportPath, originalPath)
else:
if filecmp.cmp(originalPath, exportPath, shallow=False):
print(" files identical!")
else:
for a, b in zip(
open(originalPath).readlines(),
open(exportPath).readlines()):
if a != b:
no_changes = (False,
"files differ: {}".format(testName))
print("FILES DIFFER! First line that differs:")
print("Original:", a.strip())
print("New: ", b.strip())
print("...")
time.sleep(3)
utilities.launchFile(exportPath)
utilities.launchFile(originalPath)
break
timingsPath = "renderTests/renderTimings.json.txt"
regenerateTimings = False
try:
oldTimings = json.load(open(timingsPath))
print("{:<20}{:>20}{:>20}".format("Test Name", "Previous", "New"))
for testName in sorted(timings):
try:
remark = "ok"
if timings[testName] > oldTimings[testName] * 1.1:
remark = "** slower! **"
print("{:<20}{:>19.2f}s{:>19.2f}s\t{}".format(
testName, oldTimings[testName], timings[testName], remark))
except KeyError:
print("{:<20}{:>20}s{:>19.2f}s".format(testName, "",
timings[testName]))
regenerateTimings = True
except IOError:
print("unable to load previous timings...")
if not os.path.exists(timingsPath) or regenerateTimings:
print("overwriting previous timings...")
json.dump(timings, open(timingsPath, "w"))
return no_changes, ""
def run():
timings = {}
for testName in ["mei", "inv", "ins_moleculo", "ins_pacbio", "del_chr1", "translocation"]:
print(">", testName, "<")
exportPath = "renderTests/export_{}_new.svg".format(testName)
originalPath = "renderTests/export_{}_original.svg".format(testName)
d = gzip.open("renderTests/{}.pickle.gz".format(testName), "rb")
try:
dataHub = pickle.load(d, encoding="latin1")
except TypeError:
dataHub = pickle.load(d)
dataHub.args = MockArgs()
dataHub.args.thicker_lines = False
dataHub.args.export = exportPath
dataHub.args.context = 0
t0 = time.time()
app.renderSamples(dataHub)
app.ensureExportData(dataHub)
app.runDirectExport(dataHub)
t1 = time.time()
timings[testName] = t1-t0
no_changes = True
if not os.path.exists(originalPath):
print(" first time running; nothing to compare against")
shutil.copy(exportPath, originalPath)
else:
if filecmp.cmp(originalPath, exportPath, shallow=False):
print(" files identical!")
else:
for a, b in zip(open(originalPath).readlines(), open(exportPath).readlines()):
if a != b:
no_changes = (False, "files differ: {}".format(testName))
print("FILES DIFFER! First line that differs:")
print("Original:", a.strip())
print("New: ", b.strip())
print("...")
time.sleep(3)
utilities.launchFile(exportPath)
utilities.launchFile(originalPath)
break
timingsPath = "renderTests/renderTimings.json.txt"
regenerateTimings = False
try:
oldTimings = json.load(open(timingsPath))
print("{:<20}{:>20}{:>20}".format("Test Name", "Previous", "New"))
for testName in sorted(timings):
try:
remark = "ok"
if timings[testName] > oldTimings[testName] * 1.1:
remark = "** slower! **"
print("{:<20}{:>19.2f}s{:>19.2f}s\t{}".format(testName, oldTimings[testName], timings[testName], remark))
except KeyError:
print("{:<20}{:>20}s{:>19.2f}s".format(testName, "", timings[testName]))
regenerateTimings = True
except IOError:
print("unable to load previous timings...")
if not os.path.exists(timingsPath) or regenerateTimings:
print("overwriting previous timings...")
json.dump(timings, open(timingsPath, "w"))
return no_changes, ""
if not os.path.exists(originalPath):
print " first time running; nothing to compare against"
shutil.copy(exportPath, originalPath)
else:
if filecmp.cmp(originalPath, exportPath, shallow=False):
print " files identical!"
else:
for a, b in zip(open(originalPath).readlines(), open(exportPath).readlines()):
if a != b:
print "FILES DIFFER! First line that differs:"
print "Original:", a.strip()
print "New: ", b.strip()
print "..."
time.sleep(3)
utilities.launchFile(exportPath)
utilities.launchFile(originalPath)
break
timingsPath = "tests/renderTimings.json.txt"
regenerateTimings = False
try:
oldTimings = json.load(open(timingsPath))
print "{:<20}{:>20}{:>20}".format("Test Name", "Previous", "New")
for testName in sorted(timings):
try:
remark = "ok"
if timings[testName] > oldTimings[testName] * 1.1:
remark = "** slower! **"
shutil.copy(exportPath, originalPath)
else:
if filecmp.cmp(originalPath, exportPath, shallow=False):
print " files identical!"
else:
for a, b in zip(
open(originalPath).readlines(),
open(exportPath).readlines()):
if a != b:
print "FILES DIFFER! First line that differs:"
print "Original:", a.strip()
print "New: ", b.strip()
print "..."
time.sleep(3)
utilities.launchFile(exportPath)
utilities.launchFile(originalPath)
break
timingsPath = "tests/renderTimings.json.txt"
regenerateTimings = False
try:
oldTimings = json.load(open(timingsPath))
print "{:<20}{:>20}{:>20}".format("Test Name", "Previous", "New")
for testName in sorted(timings):
try:
remark = "ok"
if timings[testName] > oldTimings[testName] * 1.1:
remark = "** slower! **"
print "{:<20}{:>19.2f}s{:>19.2f}s\t{}".format(