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 checkRequirements(args):
if not remap.check_swalign():
print "ERROR: check that svviz is correctly installed -- the 'ssw' Smith-Waterman alignment module does not appear to be functional"
sys.exit(1)
if args.export:
exportFormat = export.getExportFormat(args)
converter = export.getExportConverter(args, exportFormat)
if converter is None and exportFormat != "svg":
if args.converter is not None:
logging.error("ERROR: unable to run SVG converter '{}'. Please check that it is "
"installed correctly".format(args.converter))
else:
logging.error("ERROR: unable to export to PDF/PNG because at least one of the following "
"programs must be correctly installed: webkitToPDF, librsvg or inkscape")
sys.exit(1)
def checkRequirements(args):
if not remap.check_swalign():
print "ERROR: check that svviz is correctly installed -- the 'ssw' Smith-Waterman alignment module does not appear to be functional"
sys.exit(1)
if args.export:
exportFormat = export.getExportFormat(args)
converter = export.getExportConverter(args, exportFormat)
if converter is None and exportFormat != "svg":
if args.converter is not None:
logging.error(
"ERROR: unable to run SVG converter '{}'. Please check that it is "
"installed correctly".format(args.converter))
else:
logging.error(
"ERROR: unable to export to PDF/PNG because at least one of the following "
"programs must be correctly installed: webkitToPDF, librsvg or inkscape"
)
sys.exit(1)
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 **"
)
