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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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