class OWDtoxsAlignment(widget.OWWidget):
name = "Dtoxs Alignment"
description = "Step 1 of the Dtoxs SOP. Uses a Burrows-Wheeler Aligner (BWA)."
category = "RNASeq"
icon = "icons/dtoxs-alignment2.svg"
priority = 10
image_name = "biodepot/dtoxs_alignment"
image_version = "latest"
inputs = [("References", str, "set_refs"),
("Seqs", str, "set_seqs"),
("Configs", str, "set_configs"),
("Barcodes", str, "set_barcodes_file")]
outputs = [("Counts", str)]
auto_run = Setting(True)
want_main_area = False
def __init__(self):
super().__init__()
# Docker Client
# This client talks to your local docker
self.docker = DockerClient('unix:///var/run/docker.sock', 'local')
self.hostDirectories = {'refs': None, 'seqs': None, 'conf': None, 'counts': None, 'aligns': None, 'barcodes': None}
self.labelText = {'refs': 'References: {0}', 'seqs': 'Sequences: {0}', 'conf': 'Configs: {0}', 'barcodes': 'Barcode file: {0}'}
# folders that will created automatically
self.result_folder_name = "Counts"
self.aligns_folder_name = "Aligns"
# GUI
box = gui.widgetBox(self.controlArea, "Info")
self.lblRefs = gui.widgetLabel(box, 'References: Not Set')
self.lblSeqs = gui.widgetLabel(box, 'Sequences: Not Set')
self.lblConfigs = gui.widgetLabel(box, 'Configs: Not Set')
self.lblBarcodes = gui.widgetLabel(box, "Barcode file: Not Set")
self.infoLabel = gui.widgetLabel(box, 'Waiting...')
self.infoLabel.setWordWrap(True)
gui.checkBox(self.controlArea, self, 'auto_run', 'Run automatically when input set')
self.btn_run = gui.button(self.controlArea, self, "Run", callback=self.btn_run_pushed)
self.is_running = False
self.setMinimumSize(500, 200)
"""
Called when the user pushes 'Run'
"""
def btn_run_pushed(self):
self.start_container(run_btn_pushed=True)
"""
Set references
"""
def set_refs(self, path):
self.__set_directory__('refs', self.lblRefs, path)
"""
Set seqs
"""
def set_seqs(self, path):
self.__set_directory__('seqs', self.lblSeqs, path, startContainer=False)
if self.hostDirectories['seqs'] is not None:
# Jimmy March-28-2017, once the seq input was set, automatically create a result and aligns folder as a sibling of "Seqs"
parent_path = os.path.abspath(os.path.join(self.hostDirectories['seqs'], '..'))
self.hostDirectories['counts'] = os.path.join(parent_path, self.result_folder_name)
self.hostDirectories['aligns'] = os.path.join(parent_path, self.aligns_folder_name)
if not os.path.exists(self.hostDirectories['counts']):
os.makedirs(self.hostDirectories['counts'])
if not os.path.exists(self.hostDirectories['aligns']):
os.makedirs(self.hostDirectories['aligns'])
self.start_container(run_btn_pushed=False)
def set_configs(self, path):
self.__set_directory__('conf', self.lblConfigs, path)
def __set_directory__(self, key, ctrlLabel, path, startContainer = True):
# When a user removes a connected Directory widget,
# it sends a signal with path=None
if path is None:
self.hostDirectories[key] = None
ctrlLabel.setText(self.labelText[key].format('Not Set'))
elif not os.path.exists(path):
self.hostDirectories[key] = None
ctrlLabel.setText(self.labelText[key].format('None existent directory: {}'.format(str(path))))
else:
self.hostDirectories[key] = path.strip()
if key == 'barcodes':
path = os.path.basename(path)
self.hostDirectories['barcodes_basename'] = path
ctrlLabel.setText(self.labelText[key].format((str(path))))
if startContainer:
self.start_container(run_btn_pushed=False)
def set_barcodes_file(self, filename):
self.__set_directory__('barcodes', self.lblBarcodes, filename)
"""
Pull image
"""
def pull_image(self):
self.infoLabel.setText('Pulling \'' + self.image_name + ":" + self.image_version + '\' from Dockerhub...')
self.setStatusMessage("Downloading...")
self.progressBarInit()
self.is_running = True
self.btn_run.setEnabled(False)
# Pull the image in a new thread
self.pull_image_worker = PullImageThread(self.docker, self.image_name, self.image_version)
self.pull_image_worker.pull_progress.connect(self.pull_image_progress)
self.pull_image_worker.finished.connect(self.pull_image_finished)
self.pull_image_worker.start()
def pull_image_progress(self, val):
self.progressBarSet(val)
def pull_image_finished(self):
self.infoLabel.setText('Finished pulling \'' + self.image_name + ":" + self.image_version + '\'')
self.progressBarFinished()
self.run_container()
"""
Alignment
"""
def start_container(self, run_btn_pushed=True):
# Make sure both inputs are set
all_set = all(value is not None for value in self.hostDirectories.values())
if all_set:
if not self.is_running and (self.auto_run or run_btn_pushed):
# Make sure the docker image is downloaded
if not self.docker.has_image(self.image_name, self.image_version):
self.pull_image()
else:
self.run_container()
def run_container(self):
self.is_running = True
self.btn_run.setEnabled(False)
self.infoLabel.setText('Running alignment...')
self.setStatusMessage('Running...')
#self.progressBarInit()
# Run the container in a new thread
self.run_container_thread = RunAlignmentThread(self.docker,
self.image_name,
self.hostDirectories)
self.run_container_thread.progress.connect(self.run_container_progress)
self.run_container_thread.finished.connect(self.run_container_finished)
self.run_container_thread.start()
def run_container_progress(self, val):
self.progressBarSet(val)
def run_container_finished(self):
self.infoLabel.setText("Finished running alignment!")
self.btn_run.setEnabled(True)
self.is_running = False
self.btn_run.setText('Run again')
self.setStatusMessage('Finished!')
#self.progressBarFinished()
self.send("Counts", self.hostDirectories['counts'])
class OWRSEMCalc(widget.OWWidget):
name = "RSEM Calculation"
description = "Step2: handles both the alignment of reads against reference transcript sequences and the calculation of relative abundances. It executes rsem-calculate-expression command"
category = "RNASeq"
icon = "icons/rsemcalc.svg"
priority = 10
image_name = "genomicpariscentre/rsem"
image_version = "latest"
inputs = [(".fastq files + ref files from step1", str, "set_aligns")]
outputs = [("Results", str)]
want_main_area = False
# The directory of the alignment data needed to run
# the container will be set by the user before the
# container can be run
host_counts_dir = ""
# The default write location of all widgets should be
# ~/BioDepot/WidgetName/
# TODO is this an issue if multiple containers write to the same place?
# host_results_dir = os.path.expanduser('~') + '/BioDepot/Kallisto'
host_results_dir = os.path.expanduser('~') + '/BioDepot/RSEM_Calc/Results'
def __init__(self):
super().__init__()
# Docker Client
# This client talks to your local docker
self.docker = DockerClient('unix:///var/run/docker.sock', 'local')
# GUI
box = gui.widgetBox(self.controlArea, "Info")
self.infoLabel = gui.widgetLabel(
box, 'Connect to data or use a Directory widget'
' to specify location of UMI read data files')
self.infoLabel.setWordWrap(True)
# TODO let user specify results directory
# self.btn_res = gui.button(None, self, "Open", callback=self.set_results_dir)
# self.resultsEdit = QtGui.QLineEdit(self.host_results_dir)
# self.buttonsArea.layout().addWidget(self.btn_res)
# self.buttonsArea.layout().addWidget(self.resultsEdit)
self.autoRun = True
gui.checkBox(self.controlArea, self, 'autoRun',
'Run automatically when input set')
self.btn_run = gui.button(self.controlArea,
self,
"Run",
callback=self.start_analysis)
"""
Set input
"""
def set_aligns(self, path):
if not type(path) is str:
# TODO create warning
print('Tried to set input directory to None')
elif not os.path.exists(path):
# TODO create warning
print('Tried to set input directory to none existent directory: ' +
str(path))
else:
self.host_counts_dir = path.strip()
if self.autoRun:
self.start_analysis()
else:
self.infoLabel.setText(
'Input directory set.\nWaiting to run...')
"""
Pull image
"""
def pull_image(self):
self.infoLabel.setText('Pulling \'' + self.image_name + ":" +
self.image_version + '\' from Dockerhub...')
self.setStatusMessage("Downloading...")
self.progressBarInit()
self.btn_run.setEnabled(False)
# Pull the image in a new thread
self.pull_image_thread = PullImageThread(self.docker, self.image_name,
self.image_version)
self.pull_image_thread.pull_progress.connect(self.pull_image_progress)
self.pull_image_thread.finished.connect(self.pull_image_done)
self.pull_image_thread.start()
def pull_image_progress(self, val):
self.progressBarSet(val)
def pull_image_done(self):
self.infoLabel.setText('Finished pulling \'' + self.image_name + ":" +
self.image_version + '\'')
self.progressBarFinished()
self.run_analysis()
"""
Analysis
"""
def start_analysis(self):
# Make sure the docker image is downloaded
if not self.docker.has_image(self.image_name, self.image_version):
self.pull_image()
# Make sure there is an alignment directory set
elif self.host_counts_dir:
self.run_analysis()
else:
self.infoLabel.setText('Set directory before running.')
def run_analysis(self):
self.btn_run.setEnabled(False)
self.infoLabel.setText('Running analysis...')
self.setStatusMessage('Running...')
self.progressBarInit()
# Run the container in a new thread
self.run_analysis_thread = RunAnalysisThread(self.docker,
self.image_name,
self.host_counts_dir,
self.host_results_dir)
self.run_analysis_thread.analysis_progress.connect(
self.run_analysis_progress)
self.run_analysis_thread.finished.connect(self.run_analysis_done)
self.run_analysis_thread.start()
def run_analysis_progress(self, val):
self.progressBarSet(val)
def run_analysis_done(self):
self.infoLabel.setText("Finished running analysis!")
self.btn_run.setEnabled(True)
self.btn_run.setText('Run again')
self.setStatusMessage('Finished!')
self.progressBarFinished()
self.send("Results", self.host_results_dir)
self.btn_run.setEnabled(True)
class OWDtoxsAlignment(widget.OWWidget):
name = "Dtoxs Alignment"
description = "Step 1 of the Dtoxs SOP. Uses a Burrows-Wheeler Aligner (BWA)."
category = "RNASeq"
icon = "icons/dtoxs-alignment2.svg"
priority = 10
image_name = "biodepot/dtoxs_alignment"
image_version = "latest"
inputs = [("References", str, "set_refs"), ("Seqs", str, "set_seqs")]
outputs = [("Counts", str)]
auto_run = Setting(True)
want_main_area = False
def __init__(self):
super().__init__()
# Docker Client
# This client talks to your local docker
self.docker = DockerClient('unix:///var/run/docker.sock', 'local')
self.host_ref_dir = None
self.host_seq_dir = None
self.ref_dir_set = False
self.seq_dir_set = False
self.result_folder_name = "/Count"
self.aligns_folder_name = "/Aligns"
# TODO is this an issue if multiple containers write to the same place?
# TODO add timestamp to directory name to differentiate runs
# Jimmy, Mar/7/2017, I don't know what does "toHostDir" do. Since our DockerClient missed that code, I comment it temporary
#self.host_counts_dir = counts_dir #self.docker.toHostDir(counts_dir)
# GUI
box = gui.widgetBox(self.controlArea, "Info")
self.infoLabel = gui.widgetLabel(
box, 'Connect to a Directory widget '
'to specify location of reference '
'and seq fastq files')
self.infoLabel.setWordWrap(True)
gui.checkBox(self.controlArea, self, 'auto_run',
'Run automatically when input set')
self.btn_run = gui.button(self.controlArea,
self,
"Run",
callback=self.btn_run_pushed)
self.is_running = False
"""
Called when the user pushes 'Run'
"""
def btn_run_pushed(self):
self.start_container(run_btn_pushed=True)
"""
Set references
"""
def set_refs(self, path):
# When a user removes a connected Directory widget,
# it sends a signal with path=None
if path is None:
self.ref_dir_set = False
else:
self.host_ref_dir = path
if self.host_ref_dir is None:
# TODO emit error
self.ref_dir_set = False
print('References set to invalid directory')
else:
self.ref_dir_set = True
self.start_container(run_btn_pushed=False)
"""
Set seqs
"""
def set_seqs(self, path):
# When a user removes a connected Directory widget,
# it sends a signal with path=None
if path is None:
self.seq_dir_set = False
else:
self.host_seq_dir = path
# Jimmy March-28-2017, once the seq input was set, automatically create a result and aligns folder as a sibling of "Seqs"
parent_path = os.path.abspath(os.path.join(self.host_seq_dir,
'..'))
self.host_counts_dir = os.path.join(parent_path +
self.result_folder_name)
self.host_aligns_dir = os.path.join(parent_path +
self.aligns_folder_name)
if not os.path.exists(self.host_counts_dir):
os.makedirs(self.host_counts_dir)
if not os.path.exists(self.host_aligns_dir):
os.makedirs(self.host_aligns_dir)
if self.host_seq_dir is None:
# TODO emit error
self.seq_dir_set = False
print('Seq set to invalid directory')
else:
self.seq_dir_set = True
self.start_container(run_btn_pushed=False)
"""
Pull image
"""
def pull_image(self):
self.infoLabel.setText('Pulling \'' + self.image_name + ":" +
self.image_version + '\' from Dockerhub...')
self.setStatusMessage("Downloading...")
self.progressBarInit()
self.is_running = True
self.btn_run.setEnabled(False)
# Pull the image in a new thread
self.pull_image_worker = PullImageThread(self.docker, self.image_name,
self.image_version)
self.pull_image_worker.pull_progress.connect(self.pull_image_progress)
self.pull_image_worker.finished.connect(self.pull_image_finished)
self.pull_image_worker.start()
def pull_image_progress(self, val):
self.progressBarSet(val)
def pull_image_finished(self):
self.infoLabel.setText('Finished pulling \'' + self.image_name + ":" +
self.image_version + '\'')
self.progressBarFinished()
self.run_container()
"""
Alignment
"""
def start_container(self, run_btn_pushed=True):
# Make sure both inputs are set
if self.ref_dir_set and self.seq_dir_set:
if not self.is_running and (self.auto_run or run_btn_pushed):
# Make sure the docker image is downloaded
if not self.docker.has_image(self.image_name,
self.image_version):
self.pull_image()
else:
self.run_container()
else:
self.infoLabel.setText(
'References and Seqs directories set.\nWaiting to run...')
elif self.ref_dir_set:
self.infoLabel.setText("Waiting for user to set Seqs directory.")
elif self.seq_dir_set:
self.infoLabel.setText(
"Waiting for user to set References directory.")
def run_container(self):
self.is_running = True
self.infoLabel.setText('Running alignment...')
self.setStatusMessage('Running...')
#self.progressBarInit()
# Run the container in a new thread
self.run_container_thread = RunAlignmentThread(
self.docker, self.image_name, self.host_ref_dir, self.host_seq_dir,
self.host_counts_dir, self.host_aligns_dir)
self.run_container_thread.progress.connect(self.run_container_progress)
self.run_container_thread.finished.connect(self.run_container_finished)
self.run_container_thread.start()
def run_container_progress(self, val):
self.progressBarSet(val)
def run_container_finished(self):
self.infoLabel.setText("Finished running alignment!")
self.btn_run.setEnabled(True)
self.is_running = False
self.btn_run.setText('Run again')
self.setStatusMessage('Finished!')
#self.progressBarFinished()
self.send("Counts", self.host_counts_dir)
class OWDtoxsAnalysis(widget.OWWidget):
name = "Dtoxs Analysis"
description = "Step 2 of Dtoxs SOP. Uses edgeR for differential expression analysis."
category = "RNASeq"
icon = "icons/dtoxs-analysis2.svg"
priority = 10
image_name = "biodepot/dtoxs_analysis"
image_version = "latest"
inputs = [("Counts", str, "set_aligns", widget.Default),
("Configs", str, "set_configs"), ("Params", str, "set_params")]
outputs = [("Results", str), ("Top 40", Orange.data.Table)]
want_main_area = True
want_control_area = False
Exp_Design_file = settings.Setting('', schema_only=True)
def __init__(self):
super().__init__()
self.result_folder_name = "Results"
self.host_counts_dir = None
self.host_config_dir = None
self.host_param_dir = None
# This client talks to your local docker
self.docker = DockerClient('unix:///var/run/docker.sock', 'local')
# GUI
self.setStyleSheet("QPushButton{\n"
" background-color: #1588c5;\n"
" color: white;\n"
" height: 25px;\n"
" border: 1px solid #1a8ac6;\n"
"}")
# creat controls
self.vlayoutBase = QtWidgets.QVBoxLayout()
self.vlayoutBase.setSizeConstraint(
QtWidgets.QLayout.SetDefaultConstraint)
self.vlayoutBase.setContentsMargins(0, 0, 0, 0)
self.vlayoutBase.setSpacing(0)
self.vlayoutBase.setObjectName("vlayoutBase")
self.vlayoutBase = QtWidgets.QVBoxLayout()
self.vlayoutBase.setContentsMargins(0, 0, 0, 0)
self.vlayoutBase.setSpacing(0)
self.vlayoutBase.setObjectName("vlayoutBase")
self.verticalLayout = QtWidgets.QVBoxLayout()
self.verticalLayout.setSizeConstraint(
QtWidgets.QLayout.SetDefaultConstraint)
self.verticalLayout.setSpacing(0)
self.verticalLayout.setObjectName("verticalLayout")
self.frameTitle = QtWidgets.QFrame(self.mainArea)
self.frameTitle.setEnabled(True)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred,
QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(
self.frameTitle.sizePolicy().hasHeightForWidth())
self.frameTitle.setSizePolicy(sizePolicy)
self.frameTitle.setMinimumSize(QtCore.QSize(0, 45))
self.frameTitle.setMaximumSize(QtCore.QSize(16777215, 65))
self.frameTitle.setStyleSheet("QFrame#frameTitle{\n"
" background: #1588c5;\n"
" color: #1588c5\n"
"}")
self.frameTitle.setFrameShape(QtWidgets.QFrame.Box)
self.frameTitle.setFrameShadow(QtWidgets.QFrame.Plain)
self.frameTitle.setObjectName("frameTitle")
self.lblFormTitle = QtWidgets.QLabel(self.frameTitle)
self.lblFormTitle.setGeometry(QtCore.QRect(10, 13, 221, 21))
font = QtGui.QFont()
font.setPointSize(18)
font.setBold(False)
font.setWeight(50)
self.lblFormTitle.setFont(font)
self.lblFormTitle.setStyleSheet("\n" " color: white;\n" "")
self.lblFormTitle.setObjectName("lblFormTitle")
self.verticalLayout.addWidget(self.frameTitle)
self.mainContent = QtWidgets.QWidget(self.mainArea)
self.mainContent.setObjectName("mainContent")
self.verticalLayout_4 = QtWidgets.QVBoxLayout(self.mainContent)
self.verticalLayout_4.setContentsMargins(15, 15, 15, 15)
self.verticalLayout_4.setObjectName("verticalLayout_4")
self.vlayout_content = QtWidgets.QVBoxLayout()
self.vlayout_content.setSizeConstraint(
QtWidgets.QLayout.SetDefaultConstraint)
self.vlayout_content.setSpacing(2)
self.vlayout_content.setObjectName("vlayout_content")
self.lblExpFile = QtWidgets.QLabel(self.mainContent)
self.lblExpFile.setMinimumSize(QtCore.QSize(0, 25))
self.lblExpFile.setMaximumSize(QtCore.QSize(16777215, 25))
self.lblExpFile.setObjectName("lblExpFile")
self.vlayout_content.addWidget(self.lblExpFile)
self.horizontalLayout = QtWidgets.QHBoxLayout()
self.horizontalLayout.setSizeConstraint(
QtWidgets.QLayout.SetDefaultConstraint)
self.horizontalLayout.setContentsMargins(0, -1, -1, -1)
self.horizontalLayout.setSpacing(1)
self.horizontalLayout.setObjectName("horizontalLayout")
self.edtExpDesignFile = QtWidgets.QLineEdit(self.mainContent)
self.edtExpDesignFile.setObjectName("edtExpDesignFile")
self.horizontalLayout.addWidget(self.edtExpDesignFile)
self.btnSelectExpFile = QtWidgets.QPushButton(self.mainContent)
self.btnSelectExpFile.setMinimumSize(QtCore.QSize(24, 24))
self.btnSelectExpFile.setMaximumSize(QtCore.QSize(24, 24))
self.btnSelectExpFile.setObjectName("btnSelectExpFile")
self.horizontalLayout.addWidget(self.btnSelectExpFile)
self.vlayout_content.addLayout(self.horizontalLayout)
self.line_2 = QtWidgets.QFrame(self.mainContent)
self.line_2.setFrameShape(QtWidgets.QFrame.HLine)
self.line_2.setFrameShadow(QtWidgets.QFrame.Sunken)
self.line_2.setObjectName("line_2")
self.vlayout_content.addWidget(self.line_2)
self.lblInfoTitle = QtWidgets.QLabel(self.mainContent)
self.lblInfoTitle.setMinimumSize(QtCore.QSize(0, 25))
self.lblInfoTitle.setMaximumSize(QtCore.QSize(16777215, 25))
self.lblInfoTitle.setStyleSheet(
"background-color:qlineargradient(spread:pad, x1:0, y1:0, x2:0, y2:1, stop:0 rgba(235, 235, 235, 255), stop:1 rgba(217, 217, 217, 255));\n"
"padding-left: 3px;")
self.lblInfoTitle.setObjectName("lblInfoTitle")
self.vlayout_content.addWidget(self.lblInfoTitle)
self.line = QtWidgets.QFrame(self.mainContent)
self.line.setFrameShape(QtWidgets.QFrame.HLine)
self.line.setFrameShadow(QtWidgets.QFrame.Sunken)
self.line.setObjectName("line")
self.vlayout_content.addWidget(self.line)
self.infoLabel = QtWidgets.QLabel(self.mainContent)
self.infoLabel.setMinimumSize(QtCore.QSize(0, 45))
self.infoLabel.setStyleSheet("padding-left: 3px")
self.infoLabel.setFrameShape(QtWidgets.QFrame.NoFrame)
self.infoLabel.setAlignment(QtCore.Qt.AlignLeading
| QtCore.Qt.AlignLeft | QtCore.Qt.AlignTop)
self.infoLabel.setWordWrap(True)
self.infoLabel.setObjectName("infoLabel")
self.vlayout_content.addWidget(self.infoLabel)
self.btn_run = QtWidgets.QPushButton(self.mainContent)
self.btn_run.setMinimumSize(QtCore.QSize(90, 0))
self.btn_run.setMaximumSize(QtCore.QSize(90, 16777215))
self.btn_run.setObjectName("btn_run")
self.vlayout_content.addWidget(self.btn_run, 0, QtCore.Qt.AlignRight)
self.verticalLayout_4.addLayout(self.vlayout_content)
self.verticalLayout.addWidget(self.mainContent)
self.vlayoutBase.addLayout(self.verticalLayout)
self.mainArea.layout().addLayout(self.vlayoutBase)
self.mainArea.layout().setContentsMargins(0, 0, 0, 0)
self.mainArea.setMinimumSize(568, 246)
# events
self.btnSelectExpFile.clicked.connect(self.OnChooseExpFile)
self.btn_run.clicked.connect(self.start_analysis)
self.retranslateUi(self.mainArea)
def retranslateUi(self, Form):
_translate = QtCore.QCoreApplication.translate
Form.setWindowTitle(_translate("Widget", "Form"))
self.lblFormTitle.setText(_translate("Widget", "DTOXS Analysis"))
self.lblExpFile.setText(
_translate("Widget", "Select experiment design file:"))
self.btnSelectExpFile.setText(_translate("Widget", " ☰ "))
self.lblInfoTitle.setText(_translate("Widget", "Information"))
self.infoLabel.setText(
_translate(
"Widget",
"Connect to Dtoxs Alignment or use a Directory widget to specify location of UMI read counts data files"
))
self.btn_run.setText(_translate("Widget", "Run"))
self.edtExpDesignFile.setText(self.Exp_Design_file)
"""
Set input
"""
def set_aligns(self, path):
if not type(path) is str:
# TODO create warning
print('Tried to set alignment directory to None')
elif not os.path.exists(path):
# TODO create warning
print(
'Tried to set alignment directory to none existent directory: '
+ str(path))
else:
self.host_counts_dir = path.strip()
# Jimmy March-29-2017, once the counts input was set, automatically create an output fold as a sibling of "Seqs"
parent_path = os.path.abspath(
os.path.join(self.host_counts_dir, '..'))
self.host_results_dir = os.path.join(parent_path,
self.result_folder_name)
if not os.path.exists(self.host_results_dir):
os.makedirs(self.host_results_dir)
if os.path.exists(self.Exp_Design_file):
import shutil
shutil.copy2(self.Exp_Design_file, self.host_counts_dir)
if self.host_param_dir and self.host_config_dir and self.Exp_Design_file:
self.infoLabel.setText('All set.\nWaiting to run...')
def set_configs(self, path):
if not type(path) is str:
print('Tried to set configs directory to None')
elif not os.path.exists(path):
print(
'Tried to set configs directory to none existent directory: ' +
str(path))
else:
self.host_config_dir = path.strip()
if self.host_counts_dir and self.host_param_dir and self.Exp_Design_file:
self.infoLabel.setText('All set.\nWaiting to run...')
def set_params(self, path):
if not type(path) is str:
print('Tried to set params directory to None')
elif not os.path.exists(path):
print(
'Tried to set params directory to none existent directory: ' +
str(path))
else:
self.host_param_dir = path.strip()
if self.host_counts_dir and self.host_config_dir and self.Exp_Design_file:
self.infoLabel.setText('All set.\nWaiting to run...')
def OnChooseExpFile(self):
start_file = os.path.expanduser("~/")
filename, _ = QtWidgets.QFileDialog.getOpenFileName(
self, 'Open Experiment Design File', start_file)
if not filename:
return
self.edtExpDesignFile.setText(filename)
self.Exp_Design_file = filename
if self.host_counts_dir and self.host_config_dir and self.host_param_dir:
import shutil
shutil.copy2(self.Exp_Design_file, self.host_counts_dir)
self.infoLabel.setText('All set.\nWaiting to run...')
"""
Pull image
"""
def pull_image(self):
self.infoLabel.setText('Pulling \'' + self.image_name + ":" +
self.image_version + '\' from Dockerhub...')
self.setStatusMessage("Downloading...")
self.progressBarInit()
self.btn_run.setEnabled(False)
# Pull the image in a new thread
self.pull_image_thread = PullImageThread(self.docker, self.image_name,
self.image_version)
self.pull_image_thread.pull_progress.connect(self.pull_image_progress)
self.pull_image_thread.finished.connect(self.pull_image_done)
self.pull_image_thread.start()
def pull_image_progress(self, val):
self.progressBarSet(val)
def pull_image_done(self):
self.infoLabel.setText('Finished pulling \'' + self.image_name + ":" +
self.image_version + '\'')
self.progressBarFinished()
self.run_analysis()
"""
Analysis
"""
def start_analysis(self):
# Make sure the docker image is downloaded
if not self.docker.has_image(self.image_name, self.image_version):
self.pull_image()
# Make sure there is an alignment directory set
elif self.host_counts_dir and self.host_config_dir and self.host_param_dir:
self.run_analysis()
else:
self.infoLabel.setText(
'Set counts, params and configs directories before running.')
def run_analysis(self):
self.infoLabel.setText('Running analysis...')
self.setStatusMessage('Running...')
#self.progressBarInit()
# Run the container in a new thread
self.run_analysis_thread = RunAnalysisThread(
self.docker, self.image_name, self.host_counts_dir,
self.host_results_dir, self.host_config_dir, self.host_param_dir)
self.run_analysis_thread.analysis_progress.connect(
self.run_analysis_progress)
self.run_analysis_thread.finished.connect(self.run_analysis_done)
self.run_analysis_thread.start()
def run_analysis_progress(self, val):
self.progressBarSet(val)
def run_analysis_done(self):
self.infoLabel.setText("Finished running analysis!")
self.btn_run.setEnabled(True)
self.btn_run.setText('Run again')
self.setStatusMessage('Finished!')
#self.progressBarFinished()
self.send("Results", self.host_results_dir)
# Jimmy March 29 2017 added, create a dataset for DataTable widget to show TOP-40.tsv
tsvFile = os.path.join(self.host_results_dir, 'FDR-0.1/TOP-40.tsv')
tsvReader = FileFormat.get_reader(tsvFile)
data = None
try:
data = tsvReader.read()
# TODO Jimmy March 29 2017, tried to define domain for DataTable, didn't work
'''
domain = Orange.data.Domain(["Cell", "Plate", "Gene", "logFC", "logCPM", "PValue"], data.domain)
domain = Orange.data.Domain(data.domain.attributes, data.domain.class_vars,
[Orange.data.DiscreteVariable("Cell"),
Orange.data.DiscreteVariable("Plate"),
Orange.data.DiscreteVariable("Condition1"),
Orange.data.DiscreteVariable("Condition2"),
Orange.data.StringVariable("Gene"),
Orange.data.ContinuousVariable("logFC"),
Orange.data.ContinuousVariable("logCPM"),
Orange.data.StringVariable("PValue")])
data = data.from_table(domain, data)'''
except Exception as ex:
print(ex)
self.send("Top 40", data)
class FastQCAnalysis(widget.OWWidget):
name = "FastQC Analysis"
description = "Step 2 of Dtoxs SOP. Uses edgeR for differential expression analysis."
category = "RNASeq"
icon = "icons/dtoxs-analysis2.svg"
priority = 10
image_name = "conradstoerker/fastqc"
image_version = "latest"
inputs = [("Counts", str, "set_aligns")]
outputs = [("Results", str)]
want_main_area = False
# The directory of the alignment data needed to run
# the container will be set by the user before the
# container can be run
host_counts_dir = ""
def __init__(self):
super().__init__()
# Docker Client
# This client talks to your local docker
self.docker = DockerClient('unix:///var/run/docker.sock', 'local')
# GUI
box = gui.widgetBox(self.controlArea, "Info")
self.infoLabel = gui.widgetLabel(box, 'Connect to Dtoxs Alignment or use a Directory widget'
' to specify location of UMI read counts data files')
self.infoLabel.setWordWrap(True)
# TODO let user specify results directory
# self.btn_res = gui.button(None, self, "Open", callback=self.set_results_dir)
# self.resultsEdit = QtGui.QLineEdit(self.host_results_dir)
# self.buttonsArea.layout().addWidget(self.btn_res)
# self.buttonsArea.layout().addWidget(self.resultsEdit)
self.autoRun = True
gui.checkBox(self.controlArea, self, 'autoRun', 'Run automatically when input set')
self.btn_run = gui.button(self.controlArea, self, "Run", callback=self.start_analysis)
"""
Set input
"""
def set_aligns(self, path):
if not type(path) is str:
# TODO create warning
print('Tried to set alignment directory to None')
elif not os.path.exists(path):
# TODO create warning
print('Tried to set alignment directory to none existent directory: ' + str(path))
else:
self.host_counts_dir = path.strip()
if self.autoRun:
self.start_analysis()
else:
self.infoLabel.setText('Alignment directory set.\nWaiting to run...')
"""
Pull image
"""
def pull_image(self):
self.infoLabel.setText('Pulling \'' + self.image_name + ":" + self.image_version + '\' from Dockerhub...')
self.setStatusMessage("Downloading...")
self.progressBarInit()
self.btn_run.setEnabled(False)
# Pull the image in a new thread
self.pull_image_thread = PullImageThread(self.docker, self.image_name, self.image_version)
self.pull_image_thread.pull_progress.connect(self.pull_image_progress)
self.pull_image_thread.finished.connect(self.pull_image_done)
self.pull_image_thread.start()
def pull_image_progress(self, val=0):
self.progressBarSet(val)
def pull_image_done(self):
self.infoLabel.setText('Finished pulling \'' + self.image_name + ":" + self.image_version + '\'')
self.progressBarFinished()
self.run_analysis()
"""
Analysis
"""
def start_analysis(self):
# Make sure the docker image is downloaded
if not self.docker.has_image(self.image_name, self.image_version):
self.pull_image()
# Make sure there is an alignment directory set
elif self.host_counts_dir:
self.run_analysis()
else:
self.infoLabel.setText('Set alignment directory before running.')
def run_analysis(self):
self.infoLabel.setText('Running analysis...')
self.setStatusMessage('Running...')
self.progressBarInit()
# Run the container in a new thread
self.run_analysis_thread = RunAnalysisThread(self.docker,
self.image_name,
self.host_counts_dir,
self.host_counts_dir)
self.run_analysis_thread.analysis_progress.connect(self.run_analysis_progress)
self.run_analysis_thread.finished.connect(self.run_analysis_done)
self.run_analysis_thread.start()
def run_analysis_progress(self, val):
self.progressBarSet(val)
def run_analysis_done(self):
self.infoLabel.setText("Finished running analysis!")
self.btn_run.setEnabled(True)
self.btn_run.setText('Run again')
self.setStatusMessage('Finished!')
self.progressBarFinished()
self.send("Results", self.host_counts_dir)
class OWDtoxsAlignment(widget.OWWidget):
name = "Dtoxs Alignment"
description = "Step 1 of the Dtoxs SOP. Uses a Burrows-Wheeler Aligner (BWA)."
category = "RNASeq"
icon = "icons/dtoxs-alignment2.svg"
priority = 10
image_name = "biodepot/dtoxs_alignment"
image_version = "latest"
inputs = [("References", str, "set_refs"), ("Seqs", str, "set_seqs")]
outputs = [("Counts", str)]
auto_run = Setting(True)
want_main_area = False
def __init__(self):
super().__init__()
# Docker Client
# This client talks to your local docker
self.docker = DockerClient('unix:///var/run/docker.sock', 'local')
# The directory of the seq data needed to run
# the container will be set by the user before the
# container can be run
self.host_ref_dir = None
self.host_seq_dir = None
self.ref_dir_set = False
self.seq_dir_set = False
# The default write location of all widgets should be
# ~/BioDepot/WidgetName/
# TODO is this an issue if multiple containers write to the same place?
# TODO add timestamp to directory name to differentiate runs
counts_dir = '~/BioDepot/Dtoxs_Alignment/Counts'
if not os.path.exists(counts_dir):
os.makedirs(counts_dir)
self.host_counts_dir = self.docker.toHostDir(counts_dir)
# GUI
box = gui.widgetBox(self.controlArea, "Info")
self.infoLabel = gui.widgetLabel(
box, 'Connect to a Directory widget '
'to specify location of reference '
'and seq fastq files')
self.infoLabel.setWordWrap(True)
gui.checkBox(self.controlArea, self, 'auto_run',
'Run automatically when input set')
self.btn_run = gui.button(self.controlArea,
self,
"Run",
callback=self.btn_run_pushed)
self.is_running = False
"""
Called when the user pushes 'Run'
"""
def btn_run_pushed(self):
self.start_container(run_btn_pushed=True)
"""
Set references
"""
def set_refs(self, path):
# When a user removes a connected Directory widget,
# it sends a signal with path=None
if path is None:
self.ref_dir_set = False
else:
self.host_ref_dir = self.docker.toHostDir(path)
if self.host_ref_dir is None:
# TODO emit error
self.ref_dir_set = False
print('References set to invalid directory')
else:
self.ref_dir_set = True
self.start_container(run_btn_pushed=False)
"""
Set seqs
"""
def set_seqs(self, path):
# When a user removes a connected Directory widget,
# it sends a signal with path=None
if path is None:
self.seq_dir_set = False
else:
self.host_seq_dir = self.docker.toHostDir(path)
if self.host_seq_dir is None:
# TODO emit error
self.seq_dir_set = False
print('Seq set to invalid directory')
else:
self.seq_dir_set = True
self.start_container(run_btn_pushed=False)
"""
Pull image
"""
def pull_image(self):
self.infoLabel.setText('Pulling \'' + self.image_name + ":" +
self.image_version + '\' from Dockerhub...')
self.setStatusMessage("Downloading...")
self.progressBarInit()
self.is_running = True
self.btn_run.setEnabled(False)
# Pull the image in a new thread
self.pull_image_thread = QThread()
self.pull_image_worker = PullImageWorker(self.docker, self.image_name,
self.image_version)
self.pull_image_worker.progress[int].connect(self.pull_image_progress)
self.pull_image_worker.finished.connect(self.pull_image_finished)
self.pull_image_worker.moveToThread(self.pull_image_thread)
self.pull_image_thread.started.connect(self.pull_image_worker.work)
self.pull_image_thread.start()
@pyqtSlot(int, name="pullImageProgress")
def pull_image_progress(self, val):
self.progressBarSet(val)
@pyqtSlot(name="pullImageFinished")
def pull_image_finished(self):
self.pull_image_thread.terminate()
self.pull_image_thread.wait()
self.infoLabel.setText('Finished pulling \'' + self.image_name + ":" +
self.image_version + '\'')
self.progressBarFinished()
self.start_container()
"""
Alignment
"""
def start_container(self, run_btn_pushed=True):
# Make sure both inputs are set
if self.ref_dir_set and self.seq_dir_set:
if not self.is_running and (self.auto_run or run_btn_pushed):
# Make sure the docker image is downloaded
if not self.docker.has_image(self.image_name,
self.image_version):
self.pull_image()
else:
self.run_container()
else:
self.infoLabel.setText(
'References and Seqs directories set.\nWaiting to run...')
elif self.ref_dir_set:
self.infoLabel.setText("Waiting for user to set Seqs directory.")
elif self.seq_dir_set:
self.infoLabel.setText(
"Waiting for user to set References directory.")
def run_container(self):
self.is_running = True
self.infoLabel.setText('Running alignment...')
self.setStatusMessage('Running...')
self.progressBarInit()
# Run the container in a new thread
self.run_container_thread = QThread()
self.run_container_worker = RunAlignmentWorker(self.docker,
self.image_name,
self.host_ref_dir,
self.host_seq_dir,
self.host_counts_dir)
self.run_container_worker.progress[int].connect(
self.run_container_progress)
self.run_container_worker.finished.connect(self.run_container_finished)
self.run_container_worker.moveToThread(self.run_container_thread)
self.run_container_thread.started.connect(
self.run_container_worker.work)
self.run_container_thread.start()
@pyqtSlot(int, name="runContainerProgress")
def run_container_progress(self, val):
self.progressBarSet(val)
@pyqtSlot(name="runContainerFinished")
def run_container_finished(self):
self.run_container_thread.terminate()
self.run_container_thread.wait()
self.infoLabel.setText("Finished running alignment!")
self.btn_run.setEnabled(True)
self.is_running = False
self.btn_run.setText('Run again')
self.setStatusMessage('Finished!')
self.progressBarFinished()
self.send("Counts", self.docker.toContainerDir(self.host_counts_dir))
