def generate(self):
files = self.find_files(self.input_directory, '.fastq')
if not files:
files = self.find_files(self.input_directory, '_001.fastq')
scripts = []
for file in files:
root = file.split(os.sep)[-1]
directory = self.working_directory + os.sep + root
script = Script(root, directory, self.query, self.input_directory, self.output_directory)
pipeline = self.pipeline
if self.pipeline == 'denovota':
read_length = self.find_read_length(self.input_directory + os.sep + file)
if read_length == 150:
pipeline = 'denovota150'
else:
pipeline = 'denovota250'
print('Detected read length', read_length, 'for input', root)
script.load_pipeline(pipeline)
scripts.append(script)
return scripts
def __init__(self, parent=None):
super(ScriptEdit, self).__init__(parent)
self.current_format = 'Human'
self.script = Script()
self.textChanged.connect(self.on_text_changed)
self.setFont(monospace_font)
# For tooltips
self.context = []
def set_data(self, text, fmt):
script = None
if fmt == 'Hex' and len(text) % 2 == 0:
try:
script = Script(text.decode('hex'))
except Exception:
pass
elif fmt == 'Human':
txt, self.context = transform_human_script(text, self.gui)
script = Script.from_human(txt)
self.script = script
def __init__(self, editor=None):
super(MyScriptEdit, self).__init__(editor)
self.editor = editor
self.current_format = known_script_formats[0]
self.script = Script()
self.textChanged.connect(self.on_text_changed)
self.setFont(monospace_font)
class MyScriptEdit(QPlainTextEdit):
def __init__(self, editor=None):
super(MyScriptEdit, self).__init__(editor)
self.editor = editor
self.current_format = known_script_formats[0]
self.script = Script()
self.textChanged.connect(self.on_text_changed)
self.setFont(monospace_font)
def on_text_changed(self):
txt = str(self.toPlainText())
self.set_data(txt, self.current_format)
def copy_hex(self):
txt = self.get_data('Hex')
QApplication.clipboard().setText(txt)
def contextMenuEvent(self, e):
menu = self.createStandardContextMenu()
menu.addAction('Copy Hex', self.copy_hex)
menu.exec_(e.globalPos())
def set_format(self, fmt):
self.current_format = fmt
self.setPlainText(self.get_data())
def set_data(self, text, fmt):
script = None
if fmt == 'Hex' and len(text) % 2 == 0:
try:
script = Script(text.decode('hex'))
except Exception:
pass
elif fmt == 'Human':
txt = transform_human(text, self.editor.gui)
script = Script.from_human(txt)
self.script = script
def get_data(self, fmt=None):
if fmt is None:
fmt = self.current_format
if not self.script: return ''
if fmt == 'Hex':
return self.script.get_hex()
elif fmt == 'Human':
return self.script.get_human()
class MyScriptEdit(QPlainTextEdit):
def __init__(self, parent=None):
super(MyScriptEdit, self).__init__(parent)
self.current_format = known_script_formats[0]
self.script = Script()
self.textChanged.connect(self.on_text_changed)
self.setFont(monospace_font)
def on_text_changed(self):
txt = str(self.toPlainText())
self.set_data(txt, self.current_format)
def copy_hex(self):
txt = self.get_data('Hex')
QApplication.clipboard().setText(txt)
def contextMenuEvent(self, e):
menu = self.createStandardContextMenu()
menu.addAction('Copy Hex', self.copy_hex)
menu.exec_(e.globalPos())
def set_format(self, fmt):
self.current_format = fmt
self.setPlainText(self.get_data())
def set_data(self, text, fmt):
script = None
if fmt == 'Hex' and len(text) % 2 == 0:
try:
script = Script(text.decode('hex'))
except Exception:
pass
elif fmt == 'Human':
txt = transform_human(text)
script = Script.from_human(txt)
self.script = script
def get_data(self, fmt=None):
if fmt is None:
fmt = self.current_format
if not self.script: return ''
if fmt == 'Hex':
return self.script.get_hex()
elif fmt == 'Human':
return self.script.get_human()
def set_data(self, text, fmt):
script = None
if fmt == 'Hex' and len(text) % 2 == 0:
try:
script = Script(text.decode('hex'))
except Exception:
pass
elif fmt == 'Human':
txt, self.context = transform_human_script(text, self.gui)
script = Script.from_human(txt)
self.script = script
def main():
scripts = Script.get_scripts()
scripts_names = list(
map(lambda script: f'{script.__name__} - {script.Meta.description}',
scripts))
response = questionary.select('Which script you want to run?',
scripts_names).ask()
index = scripts_names.index(response)
script = scripts[index]
script()
def __init__(self, parent=None):
super(MyScriptEdit, self).__init__(parent)
self.current_format = known_script_formats[0]
self.script = Script()
self.textChanged.connect(self.on_text_changed)
self.setFont(monospace_font)
class ScriptEdit(QTextEdit):
"""Script editor.
Keeps an internal Script instance that it updates
with its text, and uses to convert formats.
"""
def __init__(self, parent=None):
super(ScriptEdit, self).__init__(parent)
self.current_format = 'Human'
self.script = Script()
self.textChanged.connect(self.on_text_changed)
self.setFont(monospace_font)
# For tooltips
self.context = []
def on_text_changed(self):
txt = str(self.toPlainText())
self.set_data(txt, self.current_format)
def copy_hex(self):
txt = self.get_data('Hex')
QApplication.clipboard().setText(txt)
def contextMenuEvent(self, e):
menu = self.createStandardContextMenu()
menu.addAction('Copy Hex', self.copy_hex)
menu.exec_(e.globalPos())
def set_format(self, fmt):
self.current_format = fmt
self.setPlainText(self.get_data())
def set_data(self, text, fmt):
script = None
if fmt == 'Hex' and len(text) % 2 == 0:
try:
script = Script(text.decode('hex'))
except Exception:
pass
elif fmt == 'Human':
txt, self.context = transform_human(text)
script = Script.from_human(txt)
self.script = script
def get_data(self, fmt=None):
if fmt is None:
fmt = self.current_format
if not self.script: return ''
if fmt == 'Hex':
return self.script.get_hex()
elif fmt == 'Human':
return self.script.get_human()
def event(self, e):
if e.type() == QEvent.ToolTip:
cursor = self.cursorForPosition(e.pos())
context = self.get_tooltip(cursor.position())
if not context:
QToolTip.hideText()
else:
QToolTip.showText(e.globalPos(), context)
return True
return super(ScriptEdit, self).event(e)
def get_tooltip(self, index):
"""Returns the contextual tip for the word at index."""
if index < 0 or len(self.toPlainText()) < index:
return ''
for start, end, value, match_type in self.context:
if index >= start and index < end:
return '{} ({})'.format(value, match_type)