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How to use variant_to_str method in avocado
Best Python code snippet using avocado_python
options.py
Source:options.py 
1#!/usr/bin/env python2from __future__ import print_function3import sys, os, re4from util import import_qt_modules5import_qt_modules (globals ())6from util import findColor, findIcon, use_new_api, use_new_qt, qstring_to_str, variant_to_str, setResizeMode7import util8from prop import ObjectBrowser9# --------------------------------------------------------------------------10class OptionsBox (QWidget) :11 def __init__ (self) :12 super (OptionsBox, self).__init__ ()13 self.tab_layout = QVBoxLayout ()14 self.setLayout (self.tab_layout)15 def addWidgetItem (self, widget) :16 self.tab_layout.addWidget (widget)17 def addLayoutItem (self, layout) :18 self.tab_layout.addLayout (layout)19# --------------------------------------------------------------------------20class OptionsLineEditBox (QHBoxLayout) :21 def __init__ (self, win, dlg, settings_id, title, default_value, file_dialog = False) :22 super (OptionsLineEditBox, self).__init__ ()23 self.win = win24 self.settings_id = settings_id25 self.label = QLabel ()26 self.label.setText (title)27 self.edit = QLineEdit ()28 self.addWidget (self.label)29 self.addWidget (self.edit)30 self.button = None31 if file_dialog :32 self.button = QPushButton ()33 self.button.setText ("...")34 self.addWidget (self.button)35 self.button.clicked.connect (self.buttonClick)36 # recall value37 value = self.win.settings.string (settings_id)38 if value == "" :39 value = default_value40 self.win.settings.setValue (settings_id, value) # write default value to .ini file41 self.edit.setText (value)42 dlg.accepted.connect (self.storeValue)43 def buttonClick (self) :44 value = str (QFileDialog.getOpenFileName ())45 if value != "" :46 self.edit.setText (value)47 def storeValue (self) :48 value = str (self.edit.text ())49 value = value.strip ()50 self.win.settings.setValue (self.settings_id, value)51# --------------------------------------------------------------------------52class OptionDialog (QDialog) :53 def __init__ (self, win) :54 super (OptionDialog, self).__init__ (win)55 self.win = win56 self.page_count = 057 self.current_tab = None58 "toolBar with buttons"59 self.toolBar = QToolBar ()60 self.toolBar.setOrientation (Qt.Vertical)61 "stackWidget for option pages"62 self.stackWidget = QStackedWidget ()63 "toolBar and stackWidget - central dialog area"64 self.hlayout = QHBoxLayout ()65 self.hlayout.addWidget (self.toolBar)66 self.hlayout.addWidget (self.stackWidget)67 self.buttonBox = QDialogButtonBox (QDialogButtonBox.Ok | QDialogButtonBox.Cancel)68 self.buttonBox.accepted.connect (self.accept)69 self.buttonBox.rejected.connect (self.reject)70 "ok and cancel at the bottom"71 self.vlayout = QVBoxLayout ()72 self.vlayout.addLayout (self.hlayout)73 self.vlayout.addWidget (self.buttonBox)74 self.setLayout (self.vlayout)75 def addPage (self, name, icon, widget, create_widget = None) :76 if isinstance (icon, str) :77 icon = findIcon (icon)78 if widget != None :79 self.stackWidget.addWidget (widget)80 button = QPushButton ()81 button.setText (name)82 if icon != None :83 button.setIcon (icon)84 button.setIconSize (QSize (24, 24))85 button.setMinimumSize (80, 80)86 button.widget = widget87 button.create_widget = create_widget88 button.clicked.connect (lambda param, self=self, button=button: self.openPage (button))89 self.toolBar.addWidget (button)90 def openPage (self, button) :91 if button.create_widget != None :92 if button.widget == None :93 button.widget = button.create_widget ()94 self.stackWidget.addWidget (button.widget)95 else :96 self.stackWidget.setCurrentWidget (button.widget) # show empty page97 self.show ()98 button.create_widget (button.widget)99 button.create_widget = None # do not call again100 self.stackWidget.setCurrentWidget (button.widget)101 def addSimplePage (self, name, icon) :102 box = OptionsBox ()103 box.win = self.win104 self.addPage (name, icon, box)105 self.current_page = None106 self.current_tab = box107 return box108 def addTabPage (self, name, icon) :109 page = QTabWidget ()110 self.addPage (name, icon, page)111 self.current_page = page112 self.current_tab = None113 return page114 def addTab (self, name) :115 box = OptionsBox ()116 box.win = self.win117 self.current_page.addTab (box, name)118 self.current_tab = box119 return box120 def addLineEdit (self, settings_id, title, default_value, file_dialog = False) :121 layout = OptionsLineEditBox (self.win, self, settings_id, title, default_value, file_dialog)122 self.current_tab.tab_layout.addLayout (layout)123# --------------------------------------------------------------------------124class Options (OptionDialog) :125 def __init__ (self, win) :126 super (Options, self).__init__ (win)127 self.setWindowTitle ("Options")128 self.examplePage1 ()129 self.examplePage2 ()130 def examplePage1 (self) :131 page = self.addTabPage ("edit", "edit-undo")132 tab1 = self.addTab ("first")133 edit = QLineEdit ()134 tab1.addWidgetItem (edit)135 checkBox = QCheckBox ()136 checkBox.setText ("something")137 tab1.addWidgetItem (checkBox)138 tab2 = self.addTab ("second")139 def examplePage2 (self) :140 page = self.addSimplePage ("other", "folder-new")141# --------------------------------------------------------------------------142class Notes (OptionDialog) :143 def __init__ (self, win) :144 super (Notes, self).__init__ (win)145 self.setWindowTitle ("Notes")146 self.buttonBox.setStandardButtons (QDialogButtonBox.Cancel)147 self.shortcutPage ()148 self.colorCachePage ()149 self.colorNamesPage ()150 self.iconCachePage ()151 self.pathPage ()152 self.modulePage ()153 self.toolIniPage ()154 self.iniPage ("view.ini", "clementine", self.win.settings)155 self.iniPage ("edit.ini", "tellico", self.win.session)156 # -----------------------------------------------------------------------157 def pathPage (self) :158 listView = QListWidget ()159 self.addPage ("sys path", "rosegarden", listView)160 for item in sys.path :161 listView.addItem (item)162 def modulePage (self) :163 listView = QListWidget ()164 self.addPage ("modules", "kdf", listView)165 # for item in self.win.loaded_modules :166 # listView.addItem (item)167 for item in sorted (sys.modules) :168 listView.addItem (item)169 listView.itemDoubleClicked.connect (self.showModule)170 listView.itemClicked.connect (self.alternativeShowModule)171 def showModule (self, item) :172 name = item.text ()173 ObjectBrowser (self.win, sys.modules [name])174 def alternativeShowModule (self, item) :175 mask = Qt.ShiftModifier | Qt.ControlModifier | Qt.AltModifier | Qt.MetaModifier176 mod = int (QApplication.keyboardModifiers () & mask)177 if mod == Qt.ControlModifier :178 # print ("CTRL CLICK")179 self.showModule (item)180 # -----------------------------------------------------------------------181 def resizeFirstColumn (self, treeView) :182 setResizeMode (treeView.header(), 0, QHeaderView.ResizeToContents)183 def resizeSecondColumn (self, treeView) :184 setResizeMode (treeView.header(), 1, QHeaderView.ResizeToContents)185 def colorCachePage (self) :186 treeView = QTreeWidget (self)187 treeView.setHeaderLabels (["Name", "Value"])188 self.resizeFirstColumn (treeView)189 self.addPage ("color cache", "color-management", treeView)190 for name in util.color_cache :191 self.displayColor (treeView, name, util.color_cache [name])192 treeView.sortByColumn (0, Qt.AscendingOrder)193 def colorNamesPage (self) :194 treeView = QTreeWidget (self)195 treeView.setHeaderLabels (["Name", "Value"])196 self.resizeFirstColumn (treeView)197 self.addPage ("color names", "gimp", treeView)198 for name in util.color_map :199 self.displayColor (treeView, name, util.color_map [name])200 treeView.sortByColumn (0, Qt.AscendingOrder)201 def displayColor (self, branch, name, color) :202 node = QTreeWidgetItem (branch)203 node.setText (0, name)204 node.setToolTip (0, name)205 if color.lightness () < 220 and color.alpha () != 0 :206 node.setForeground (0, color)207 node.setData (0, Qt.DecorationRole, color)208 node.setText (1, str (color.red ()) + ", " + str (color.green ())+ ", " + str (color.blue ()))209 # -----------------------------------------------------------------------210 def iconCachePage (self) :211 treeView = QTreeWidget (self)212 self.addPage ("icon cache", "choqok", treeView)213 for name in util.icon_cache :214 icon = util.icon_cache [name]215 self.displayIcon (treeView, name, icon)216 treeView.sortByColumn (0, Qt.AscendingOrder)217 def displayIcon (self, branch, name, icon) :218 node = QTreeWidgetItem (branch)219 node.setText (0, name)220 node.setToolTip (0, name)221 node.setIcon (0, icon)222 # -----------------------------------------------------------------------223 def iniPage (self, name, icon, ini) :224 treeView = QTreeWidget (self)225 treeView.setHeaderLabels (["Name", "Value"])226 self.resizeFirstColumn (treeView)227 self.addPage (name, icon, treeView)228 for group in ini.childGroups () :229 branch = QTreeWidgetItem (treeView)230 branch.setText (0, "[" + group + "]")231 branch.setIcon (0, findIcon ("folder"))232 ini.beginGroup (group)233 for key in ini.childKeys () :234 value = ini.value (key)235 item = QTreeWidgetItem (branch)236 item.setText (0, key)237 item.setText (1, variant_to_str (value))238 ini.endGroup ()239 # -----------------------------------------------------------------------240 def toolIniPage (self) :241 treeView = QTreeWidget (self)242 treeView.setHeaderLabels (["Name", "Value"])243 self.resizeFirstColumn (treeView)244 self.addPage ("tools.ini", "tools-wizard", treeView)245 ini = self.win.commands246 section = None247 start = ""248 for group in ini.childGroups () :249 m = re.match ("(\w\w*)-.*", group)250 if m :251 new_start = m.group (1)252 if new_start != start :253 start = new_start254 section = QTreeWidgetItem (treeView)255 section.setText (0, start);256 section.setIcon (0, findIcon ("folder-yellow"))257 branch = QTreeWidgetItem (section)258 else :259 start = ""260 section = None261 branch = QTreeWidgetItem (treeView)262 branch.setText (0, "[" + group + "]")263 branch.setIcon (0, findIcon ("folder"))264 ini.beginGroup (group)265 for key in ini.childKeys () :266 value = ini.value (key)267 item = QTreeWidgetItem (branch)268 item.setText (0, key)269 item.setText (1, variant_to_str (value))270 ini.endGroup ()271# --------------------------------------------------------------------------272 def shortcutPage (self) :273 treeView = QTreeWidget ()274 treeView.setHeaderLabels (["Name", "Shortcut", "Invisible"])275 self.name_column = 0276 self.key_column = 1277 self.invisible_column = 2278 self.resizeFirstColumn (treeView)279 self.resizeSecondColumn (treeView)280 header = treeView.header ()281 header.hideSection (self.invisible_column)282 # name_column = 0283 # header.setSectionResizeMode (name_column, QHeaderView.ResizeToContents)284 self.addPage ("shortcuts", "key-enter", treeView)285 for item in self.win.menuBar().actions() :286 self.displayMainMenuAction (treeView, item)287 prefix = "Menu " + item.text () + " / "288 for action in item.menu().actions() :289 self.displayAction (treeView, action, prefix)290 for action in self.win.actions() :291 self.showItem (branch, action)292 for item in self.win.children() :293 if isinstance (item, QShortcut) :294 self.displayShortcut (treeView, item)295 inx = treeView.topLevelItemCount () - 1296 while inx > 0 :297 item = treeView.topLevelItem (inx)298 if item.text (1) == "" :299 treeView.takeTopLevelItem (inx)300 inx = inx - 1301 self.setKeys (treeView)302 treeView.sortByColumn (self.invisible_column, Qt.AscendingOrder)303 def displayMainMenuAction (self, treeView, item) :304 node = QTreeWidgetItem (treeView)305 text = str (item.text ())306 node.setText (self.name_column, "Menu " +text)307 inx = text.find ('&')308 if inx >= 0 and inx+1 < len (text) :309 c = text [inx+1]310 node.setText (1, "Alt+" + c.upper ())311 icon = item.icon ()312 node.setIcon (self.name_column, icon)313 def displayAction (self, treeView, action, prefix = "") :314 for shortcut in action.shortcuts () :315 node = QTreeWidgetItem (treeView)316 node.setText (self.name_column, prefix + action.text())317 node.setIcon (self.name_column, action.icon ())318 node.setText (self.key_column, self.keySequenceToString (shortcut))319 def displayShortcut (self, treeView, shortcut) :320 node = QTreeWidgetItem (treeView)321 node.setText (self.name_column, shortcut.objectName ())322 node.setText (self.key_column, self.keySequenceToString (shortcut.key()))323 def keySequenceToString (self, shortcut) :324 text = shortcut.toString ()325 text = qstring_to_str (text)326 text = text.replace ("Meta+", "Win+")327 return text328 def setKeys (self, treeView) :329 cnt = treeView.topLevelItemCount ()330 for inx in range (cnt) :331 item = treeView.topLevelItem (inx)332 text = str (item.text (self.key_column))333 key = "T"334 if text == "" :335 key = "Z"336 if text.startswith ("Win+") :337 key = key + "W"338 text = text [4:]339 else :340 key = key + "Z"341 if text.startswith ("Alt+") :342 key = key + "A"343 text = text [4:]344 else :345 key = key + "Z"346 if text.startswith ("Ctrl+") :347 key = key + "C"348 text = text [5:]349 else :350 key = key + "Z"351 if text.startswith ("Shift+") :352 key = key + "S"353 text = text [6:]354 else :355 key = key + "Z"356 if text == "Left" :357 key = key + "a"358 elif text == "Right" :359 key = key + "b"360 elif text == "Up" :361 key = key + "c"362 elif text == "Down" :363 key = key + "d"364 elif text == "Ins" :365 key = key + "e"366 elif text == "Del" :367 key = key + "f"368 elif text == "Home" :369 key = key + "g"370 elif text == "End" :371 key = key + "h"372 elif text == "PgUp" :373 key = key + "i"374 elif text == "PgDown" :375 key = key + "j"376 elif text.startswith ("F") and len (text) > 1 :377 if len (text) == 2 :378 key = key + "l"379 else :380 key = key + "m"381 elif len (text) > 1 :382 key = key + "k" # before F1 and F10383 elif text >= "0" and text <= "9":384 key = key + "o"385 elif text >= "A" and text <= "Z":386 key = key + "p"387 else:388 key = key + "n" # before digits389 key = key + text390 item.setText (self.invisible_column, key)391# --------------------------------------------------------------------------...
vcf_to_matrix.py
Source:vcf_to_matrix.py
...7from unittest.mock import patch, Mock8import logging9logger = logging.getLogger(__name__)10logger.addHandler(logging.StreamHandler())11def variant_to_str(variant):12 return f"{variant.CHROM}:{variant.start + 1}-{variant.end + 1}"13def decide_missing_query(variant: vcf.model._Record, source_vcf_reader: vcf.Reader):14 """15 Sees if a given variant (reported as missing is the evaluation vcf) is present in a given source vcf, with a missing or HOM_REF gt.16 This also throws an error if the given variant is called in the source vcf.17 """18 looked_up_variants = list(source_vcf_reader.fetch(variant.CHROM, variant.start, variant.end - 1))19 if len(looked_up_variants) == 0:20 #set_truth_zero += 121 return 022 elif len(looked_up_variants) == 1:23 if looked_up_variants[0].samples[0].gt_type == 0:24 return 025 elif looked_up_variants[0].samples[0].gt_type is None:26 return 327 else:28 raise Exception(f"variant {variant_to_str(variant)}"29 f" is not genotyped in the evaluation vcf, but is in {source_vcf_reader.filename}")30 else:31 raise Exception(f"More than one variant found with position {variant_to_str(variant)} in {source_vcf_reader.filename}")32 # because we remove/merge multiallelics from truth33def get_dosage_matrix_entry(variants, truth_vcf, query_vcf):34 pass35def decide_missing_truth(truth_data: vcf.model._Call.data, variant: vcf.model._Record):36 if truth_data.GT ==".":37 return 338 elif truth_data.GT == "0/0":39 return 040 else:41 raise Exception(f"variant {variant_to_str(variant)} has no decision in truth, but is neither ./. nor 0/0")42def get_dosage_matrix(eval_vcf: str, truth_vcf: str, query_vcf: str) -> List[List[int]]:43 """44 Creates 4*4 matrix with the query vcf dosages as rows and truth vcf as columns (0 indexed).45 The last column and row also represents uncalled genotypes.46 NOTE: the eval vcf must be the result of `rtg vcfeval` using the output mode of ga4gh.47 """48 matrix = [[0]*4 for _ in range(4)]49 vcf_eval_dosage = 050 set_truth_zero = 051 many_reprs = 052 eval_vcf_reader = vcf.Reader(filename=eval_vcf)53 truth_vcf_reader = vcf.Reader(filename=truth_vcf)54 query_vcf_reader = vcf.Reader(filename=query_vcf)55 for variants in chunk_by(eval_vcf_reader, lambda x: x.INFO['BS'] if 'BS' in x.INFO.keys() else x.POS):56 def increment_matrix(truth_dosage, query_dosage):57 """58 Increments the result matrix.59 NOTE: `None` represents no genotype recorded60 """61 logger.debug(f"Setting truth={truth_dosage} query={query_dosage} for variants {list(map(variant_to_str, variants))}")62 if truth_dosage is None:63 truth_dosage = 364 if query_dosage is None:65 query_dosage = 366 # Matrix has rows of test dosages and columns of truth dosages67 matrix[query_dosage][truth_dosage] += 168 assert len(variants) != 069 if len(variants) == 1:70 variant = variants[0]71 truth = variant.genotype("TRUTH")72 truth_eval = truth.data.BD73 truth_dosage = truth.gt_type74 query = variant.genotype("QUERY")75 query_eval = query.data.BD76 query_dosage = query.gt_type77 if truth_eval is not None and query_eval is not None:78 vcf_eval_dosage += 179 increment_matrix(truth_dosage, query_dosage)80 elif truth_eval is None and query_eval is not None:81 increment_matrix(decide_missing_truth(truth.data, variant), query_dosage)82 elif truth_eval is not None and query_eval is None:83 increment_matrix(truth_dosage, decide_missing_query(variant, query_vcf_reader))84 else:85 increment_matrix(decide_missing_truth(truth.data, variant), decide_missing_query(variant, query_vcf_reader))86 elif len(variants) == 2:87 bds = list(map(88 lambda x: variants[x[0]].genotype(x[1]).data.BD,89 itertools.product((1, 0), ("TRUTH", "QUERY"))90 ))91 gt_types = list(map(92 lambda x: variants[x[0]].genotype(x[1]).gt_type,93 itertools.product((1, 0), ("TRUTH", "QUERY"))94 ))95 if not (96 (bds[0], bds[3]) == (None, None) and None not in (bds[1], bds[2]) or97 (bds[1], bds[2]) == (None, None) and None not in (bds[0], bds[3])98 ):99 #raise Exception(f"Invalid double variant record at {variant_to_str(variants[0])} and {variant_to_str(variants[1])}")100 logger.debug(f"Invalid double variant record at {variant_to_str(variants[0])} and {variant_to_str(variants[1])}") #nearby SNPs have the same BS as well101 truth_dosage = gt_types[0] if gt_types[2] is None else gt_types[2]102 query_dosage = gt_types[1] if gt_types[3] is None else gt_types[3]103 many_reprs += 1104 increment_matrix(truth_dosage, query_dosage)105 else:106 raise Exception(f"Many variants with the same postions. First one is at {variant_to_str(variants[0])}")107 print(f"vcf_eval_dosage: {vcf_eval_dosage}, set_truth_zero: {set_truth_zero}, many_reprs: {many_reprs}")108 return matrix109x = TypeVar("x")110def chunk_by(iterable: Iterable[x], predicate: Callable[[x], Any]) -> Iterable[List[x]]:111 iterator = iter(iterable)112 chunk = [next(iterator)]113 chunk_property = predicate(chunk[0])114 for entry in iterator:115 current_property = predicate(entry)116 if chunk_property == current_property:117 chunk.append(entry)118 else:119 yield chunk120 chunk = [entry]...
file_tree.py
Source:file_tree.py
1import sys2from PyQt5.QtCore import *3from PyQt5.QtGui import *4from PyQt5.QtWidgets import *5def variant_to_str (v) :6 if sys.version_info >= (3, 0) :7 return v8 else :9 v.toString ()10def bytes_to_str (data) :11 if sys.version_info >= (3, 0) :12 return str (data, "latin1")13 else:14 return str (data)15class Window (QMainWindow) :16 def __init__ (self, parent = None) :17 super (Window, self).__init__ (parent)18 self.tree = QTreeWidget ()19 self.tree.itemDoubleClicked.connect (self.itemClick)20 self.tab = QTabWidget ()21 splitter = QSplitter (self)22 splitter.addWidget (self.tree)23 splitter.addWidget (self.tab)24 self.setCentralWidget (splitter)25 self.displayDir (self.tree, "..")26 def displayDir (self, target, path) :27 localDir = QDir (path)28 directory = QDir (localDir.absolutePath ())29 item = QTreeWidgetItem (target)30 item.setText (0, directory.dirName ())31 item.setToolTip (0, directory.absolutePath ())32 item.setData (0, Qt.UserRole, directory.absolutePath ())33 item.setForeground (0, QColor ("red"))34 infoList = directory.entryInfoList (QDir.Files | QDir.Dirs |35 QDir.NoDotAndDotDot)36 for info in infoList :37 if info.isDir () :38 self.displayDir (item, info.filePath ())39 else :40 node = QTreeWidgetItem (item)41 node.setText (0, info.fileName ())42 node.setToolTip (0, info.filePath ())43 node.setData (0, Qt.UserRole, info.filePath ())44 node.setForeground (0, QColor ("blue"))45 def itemClick (self, item, column) :46 path = variant_to_str (item.data (0, Qt.UserRole))47 info = QFileInfo (path)48 ext = "." + info.completeSuffix ()49 widget = None50 if ext in [ ".h", ".cpp", ".py" ] :51 widget = QTextEdit ()52 f = QFile (path)53 if f.open (QFile.ReadOnly) :54 data = bytes_to_str (f.readAll ())55 widget.setText (data)56 if widget != None :57 self.tab.addTab (widget, info.fileName ())58if __name__ == "__main__" :59 app = QApplication (sys.argv)60 win = Window ()61 win.show ()...
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