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run_pasta_gui.py
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run_pasta_gui.py
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"""Main script for PASTA GUI on Windows/Mac/Linux
"""
# This file is part of PASTA which is forked from SATe
# PASTA, like SATe is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# Jiaye Yu and Mark Holder, University of Kansas
import os
import platform
import subprocess
import tempfile
import sys
import time
import wx
import string
from pasta import PROGRAM_AUTHOR
from pasta import PROGRAM_INSTITUTE
from pasta import PROGRAM_DESCRIPTION
from pasta import PROGRAM_LICENSE
from pasta import PROGRAM_NAME
from pasta import PROGRAM_VERSION
from pasta import PROGRAM_WEBSITE
from pasta import PROGRAM_YEAR
from pasta import GLOBAL_DEBUG
from pasta import DEFAULT_MAX_MB
try:
from configparser import RawConfigParser
except:
from ConfigParser import RawConfigParser
from pasta import pasta_is_frozen
from pasta import pasta_home_dir
from pasta.configure import get_invoke_run_pasta_command
from pasta.tools import AlignerClasses
from pasta.tools import MergerClasses
from pasta.tools import TreeEstimatorClasses
from pasta.tools import get_aligner_classes, get_merger_classes, get_tree_estimator_classes
from pasta import filemgr
from pasta.usersettingclasses import get_list_of_seq_filepaths_from_dir
from pasta.alignment import summary_stats_from_parse
from pasta.mainpasta import get_auto_defaults_from_summary_stats
WELCOME_MESSAGE = "%s %s, %s\n\n"% (PROGRAM_NAME, PROGRAM_VERSION, PROGRAM_YEAR)
GRID_VGAP = 8
GRID_HGAP = 8
PARSING_FILES_IN_GUI = True
MAX_NUM_CPU = 16
PASTA_GUI_ONLY_PRINTS_CONFIG = os.environ.get('PASTA_GUI_ONLY_PRINTS_CONFIG') == '1'
def is_valid_int_str(s, min_v, max_v):
try:
i = int(s)
except:
return False
si = str(i)
if si != s:
return False
if min_v is not None and i < min_v:
return False
if max_v is not None and i > max_v:
return False
return True
class RangedIntValidator(wx.PyValidator):
def __init__(self, min_v, max_v):
wx.PyValidator.__init__(self)
self.min_v = min_v
self.max_v = max_v
self.Bind(wx.EVT_CHAR, self.OnChar)
def Clone(self):
return RangedIntValidator(self.min_v, self.max_v)
def is_valid_str(self, s):
return is_valid_int_str(s, self.min_v, self.max_v)
def Validate(self, win):
v = win.GetValue()
return self.is_valid_str(v)
def OnChar(self, event):
key = event.GetKeyCode()
textCtrl = self.GetWindow()
if key == wx.WXK_BACK or key == wx.WXK_DELETE:
textCtrl.SetBackgroundColour("white")
event.Skip()
return
if key < wx.WXK_SPACE or key > 255:
textCtrl.SetBackgroundColour("white")
event.Skip()
return
if chr(key) in string.digits:
textCtrl.SetBackgroundColour("white")
event.Skip()
return
if not wx.Validator_IsSilent():
wx.Bell()
# Returning without calling even.Skip eats the event before it
# gets to the text control
return
def TransferToWindow(self):
return True
def TransferFromWindow(self):
return True
class PastaFrame(wx.Frame):
def __init__(self, size):
wx.Frame.__init__(self, None, -1, "PASTA - Practical Alignment using SATe and TraAnsitivity", size=(640,480), style=wx.DEFAULT_FRAME_STYLE)
self.SetBackgroundColour(wx.LIGHT_GREY)
self.statusbar = self.CreateStatusBar()
self.statusbar.SetStatusText("PASTA Ready!")
if wx.Platform == "__WXMSW__" or wx.Platform == "__WXMAC__":
import base64
import io
icon = wx.EmptyIcon()
icon.CopyFromBitmap(wx.BitmapFromImage(wx.ImageFromStream(io.BytesIO(base64.b64decode(ICO_STR)))))
self.SetIcon(icon)
self.ctrls = []
sizer_all = wx.BoxSizer(wx.VERTICAL)
self.sizer_tool_settings = self._create_tools_sizer()
self.sizer_data = self._create_data_sizer()
self.sizer_pasta_settings = self._create_pasta_settings_sizer()
self.sizer_job_settings = self._create_job_settings_sizer()
self.sizer_workflow_settings = self._create_workflow_settings_sizer()
sizer1 = wx.BoxSizer(wx.VERTICAL)
sizer1.Add(self.sizer_tool_settings, 0, wx.EXPAND|wx.BOTTOM|wx.RIGHT, 5)
sizer1.Add(self.sizer_data, 0, wx.EXPAND|wx.TOP|wx.RIGHT, 5)
sizer1.Add(self.sizer_workflow_settings, 0, wx.EXPAND|wx.TOP|wx.RIGHT, 5)
self.sizer_settings = wx.BoxSizer(wx.HORIZONTAL)
self.sizer_settings.Add(sizer1, 0, wx.EXPAND|wx.ALL, 0)
sizer2 = wx.BoxSizer(wx.VERTICAL)
sizer2.Add(self.sizer_job_settings, 0, wx.EXPAND|wx.ALL, 0)
sizer2.Add(self.sizer_pasta_settings, 0, wx.EXPAND|wx.ALL, 0)
self.sizer_settings.Add(sizer2, 0, wx.EXPAND|wx.ALL, 0)
sizer_all.Add(self.sizer_settings, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 10)
self.button = wx.Button(self, label="Start")
self.log = wx.TextCtrl(self, -1, "", size=(200,120),style=wx.TE_MULTILINE|wx.TE_READONLY|wx.TE_RICH2)
self.log.AppendText(WELCOME_MESSAGE)
self.log.AppendText("Running Log (%s %s)\n\n" % (time.strftime("%Y-%m-%d %H:%M:%S"), time.tzname[0]))
sizer_all.Add(self.button, 0, wx.BOTTOM|wx.ALIGN_CENTER, 10)
sizer_all.Add(self.log, 4, wx.EXPAND)
self.SetAutoLayout(True)
self.Layout()
self.SetSizerAndFit(sizer_all)
self._create_menu()
self.process = None
self.process_cfg_file = None
self.Bind(wx.EVT_IDLE, self.OnIdle)
self.Bind(wx.EVT_END_PROCESS, self.OnProcessEnded)
self.Bind(wx.EVT_BUTTON, self.OnButton, self.button)
self.set_char_model() # this fixes the model based on the current default tree estimator
def _create_job_settings_sizer(self):
staticboxsizer = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Job Settings"), wx.VERTICAL)
sizer = wx.GridBagSizer(GRID_VGAP, GRID_HGAP)
cr = 0
sizer.Add(wx.StaticText(self, -1, "Job Name"),(cr,0), flag=wx.ALIGN_LEFT )
self.txt_jobname = wx.TextCtrl(self,-1,"pastajob")
sizer.Add(self.txt_jobname, (cr,1), flag=wx.EXPAND)
cr += 1
self.outputdir_btn = wx.Button(self, label="Output Dir." )
sizer.Add(self.outputdir_btn,(cr,0), flag=wx.ALIGN_LEFT )
self.txt_outputdir = wx.TextCtrl(self, -1, "", size=(250,9))
sizer.Add(self.txt_outputdir, (cr,1), flag=wx.EXPAND)
cr += 1
sizer.Add(wx.StaticText(self, -1, "CPU(s) Available"), (cr,0), flag=wx.ALIGN_LEFT )
self.cb_ncpu = wx.ComboBox(self, -1, "1", choices=list(map(str, list(range(1, MAX_NUM_CPU + 1)))), style=wx.CB_READONLY)
sizer.Add(self.cb_ncpu, (cr,1), flag=wx.EXPAND)
cr += 1
sizer.Add(wx.StaticText(self, -1, "Max. Memory (MB)"), (cr,0), flag=wx.ALIGN_LEFT )
self.txt_maxmb = wx.TextCtrl(self, -1, str(DEFAULT_MAX_MB))
sizer.Add(self.txt_maxmb, (cr,1), flag=wx.EXPAND)
staticboxsizer.Add(sizer, 0, wx.CENTER, 0)
self.Bind(wx.EVT_BUTTON, self.OnChooseOutputDir, self.outputdir_btn)
return staticboxsizer
def validate_max_mb(self, value):
try:
mb = int(value)
if mb <= 0:
raise ValueError
return True
except ValueError:
wx.MessageBox("Invalid value for Maximum MB: '" + value + "': require positive integer value.",
"Invalid Value for Maximum MB",
wx.OK|wx.ICON_EXCLAMATION)
return False
def OnChooseOutputDir(self, event):
dialog = wx.DirDialog(None, "Choose directory for output", style=wx.FD_OPEN)
dialog.ShowModal()
self.txt_outputdir.SetValue( dialog.GetPath() )
def _set_custom_pasta_settings(self, event):
#self.cb_sate_presets.SetValue("(custom)")
pass
def _create_tools_sizer(self):
from pasta.configure import get_configuration
cfg = get_configuration()
staticboxsizer = wx.StaticBoxSizer(wx.StaticBox(self, -1, "External Tools"), wx.VERTICAL)
sizer = wx.FlexGridSizer(0, 2, GRID_VGAP, GRID_HGAP)
items = ["Aligner", "Merger", "TreeEstimator"]
tool_list_list = [get_aligner_classes(), get_merger_classes(), get_tree_estimator_classes()]
self.raxml_dna_models = ["GTRCAT", "GTRGAMMA", "GTRGAMMAI"]
self.fasttree_dna_models = ["GTR+G20", "GTR+CAT", "JC+G20", "JC+CAT"]
prot_matrix = ["DAYHOFF", "DCMUT", "JTT", "MTREV", "WAG", "RTREV", "CPREV", "VT", "BLOSUM62", "MTMAM", "LG"]
prot_type = ["PROTCAT", "PROTCATI", "PROTGAMMA", "PROTGAMMAI"]
self.raxml_prot_models = [j+i for i in prot_matrix for j in prot_type]
self.raxml_prot_models.extend([j+i+"F" for i in prot_matrix for j in prot_type])
self.fasttree_prot_models = ["JTT+G20", "JTT+CAT", "WAG+G20", "WAG+CAT"]
if GLOBAL_DEBUG:
defaults = {"Aligner":"PADALIGNER", "Merger":"PADALIGNER", "TreeEstimator":"RANDTREE"}
else:
defaults = {"Aligner":"MAFFT", "Merger":"MUSCLE", "TreeEstimator":"FASTTREE"}
self.cb_tools = {}
for item_idx, item in enumerate(items):
text = wx.StaticText(self, -1, "Tree Estimator") if item == "TreeEstimator" else wx.StaticText(self, -1, item)
sizer.Add(text, 0, wx.LEFT)
tool_list = tool_list_list[item_idx]
active_tool_name_list = []
for tool in tool_list:
try:
tool_attr_name = tool.section_name.split()[0].lower()
tool_path = getattr(cfg, tool_attr_name).path
if os.path.exists(tool_path):
active_tool_name_list.append(tool_attr_name.upper())
else:
print("WARNING: tool %s not found at %s" %(tool,tool_path))
except :
raise
combobox = wx.ComboBox(self, -1, defaults[item], (-1,-1), (-1,-1), active_tool_name_list, wx.CB_READONLY)
self.cb_tools[item.lower()] = combobox
self.ctrls.append(self.cb_tools[item.lower()])
sizer.Add(combobox, 0, wx.EXPAND)
self.Bind(wx.EVT_COMBOBOX, self.OnTreeEstimatorChange, self.cb_tools["treeestimator"])
combobox = wx.ComboBox(self, -1, "GTRCAT", (-1,-1), (-1,-1), self.raxml_dna_models, wx.CB_READONLY)
self.cb_tools["model"] = combobox
self.ctrls.append(self.cb_tools["model"])
sizer.Add(wx.StaticText(self, -1, "Model"), wx.LEFT)
sizer.Add(combobox, 0, wx.EXPAND)
staticboxsizer.Add(sizer, 0, wx.CENTER, 0)
return staticboxsizer
def _create_data_sizer(self):
staticboxsizer = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Sequences and Tree"), wx.VERTICAL)
sizer = wx.FlexGridSizer(0, 2, GRID_VGAP, GRID_HGAP)
self.datatype = wx.ComboBox(self, -1, "DNA", (-1, -1), (-1, -1), ["DNA", "RNA", "Protein"], wx.CB_READONLY)
self.seq_btn = wx.Button(self, label="Sequence file ..." )
self.tree_btn = wx.Button(self, label="Tree file (optional) ..." )
self.txt_seqfn = wx.TextCtrl(self,-1)
self.txt_treefn = wx.TextCtrl(self,-1)
self.cb_multilocus = wx.CheckBox(self, -1, "Multi-Locus Data")
self.cb_multilocus.Disable()
self.checkbox_aligned = wx.CheckBox(self, -1, "Use for inital tree")
self.checkbox_aligned.SetValue(False)
self._could_be_aligned = False
self.checkbox_aligned.Disable()
sizer.AddMany([ (self.seq_btn, 0, wx.LEFT|wx.EXPAND),
(self.txt_seqfn, 0),
(wx.StaticText(self, -1, ""), 0, wx.EXPAND),
(self.cb_multilocus, 1, wx.EXPAND),
(wx.StaticText(self, -1, "Data Type"), 0, wx.ALIGN_RIGHT),
(self.datatype, 0),
(wx.StaticText(self, -1, "Initial Alignment"), 0, wx.ALIGN_RIGHT),
(self.checkbox_aligned, 0),
(self.tree_btn, 0, wx.LEFT|wx.EXPAND),
(self.txt_treefn, 0),
])
self.ctrls.extend([self.seq_btn,
self.txt_seqfn,
self.tree_btn,
self.txt_treefn,
self.datatype])
staticboxsizer.Add(sizer, 0, wx.CENTER, 0)
self.Bind(wx.EVT_BUTTON, self.OnChooseSeq, self.seq_btn)
self.Bind(wx.EVT_BUTTON, self.OnChooseTree, self.tree_btn)
self.Bind(wx.EVT_COMBOBOX, self.OnDataType, self.datatype)
self.Bind(wx.EVT_CHECKBOX, self.OnMultiLocus, self.cb_multilocus)
return staticboxsizer
def _create_workflow_settings_sizer(self):
"""
returns a wx.StaticBoxSizer with the widgets that control pre and post
processing of PASTA output.
"""
staticboxsizer = wx.StaticBoxSizer(wx.StaticBox(self, -1, "Workflow Settings"), wx.VERTICAL)
sizer = wx.GridBagSizer(GRID_VGAP, GRID_HGAP)
self.two_phase = wx.CheckBox(self, -1, "Two-Phase (not PASTA)")
self.two_phase.Value = False
self.raxml_after = wx.CheckBox(self, -1, "Extra RAxML Search")
self.raxml_after.Value = False
#self.trusted_data = wx.CheckBox(self, -1, "Trusted Data")
#self.trusted_data.Value = True
self.ctrls.extend([self.two_phase,
])
cr = 0
sizer.Add(wx.StaticText(self, -1, "Algorithm"), (cr,0), flag=wx.ALIGN_LEFT )
sizer.Add(self.two_phase, (cr,1), flag=wx.EXPAND)
cr += 1
sizer.Add(wx.StaticText(self, -1, "Post-Processing"), (cr,0), flag=wx.ALIGN_LEFT )
sizer.Add(self.raxml_after, (cr,1), flag=wx.EXPAND)
#cr += 1
#sizer.Add(wx.StaticText(self, -1, "Input Validation"), (cr,0), flag=wx.ALIGN_LEFT )
#sizer.Add(self.trusted_data, (cr,1), flag=wx.EXPAND)
self.Bind(wx.EVT_CHECKBOX, self.OnTwoPhase, self.two_phase)
staticboxsizer.Add(sizer, 0, wx.ALL, 0)
return staticboxsizer
def _create_pasta_settings_sizer(self):
staticboxsizer = wx.StaticBoxSizer(wx.StaticBox(self, -1, "PASTA Settings"), wx.VERTICAL)
sizer = wx.GridBagSizer(GRID_VGAP, GRID_HGAP)
# preset_choices = ["SATe-II-fast", "SATe-II-ML", "SATe-II-simple", "(Custom)",]
# self.cb_sate_presets = wx.ComboBox(self,
# -1,
# "SATe-II-ML",
# choices=preset_choices,
# style=wx.CB_READONLY)
tree_and_alignment_choices = ["Final", "Best"]
self.cb_tree_and_alignment = wx.ComboBox(self,
-1,
tree_and_alignment_choices[0],
choices=tree_and_alignment_choices,
style=wx.CB_READONLY)
timelimit_list = list(map(str, [i/100.0 for i in range(1,10)] + [i/10.0 for i in range(1,10)] + list(range(1,73))))
iterlimit_list = list(map(str, [1, 5, 10, 20, 50, 100, 200, 500, 1000]))
self.rb_maxsub1 = wx.RadioButton(self, -1, "Percentage", name="frac", style=wx.RB_GROUP)
self.rb_maxsub2 = wx.RadioButton(self, -1, "Size", name="size")
self.cb_maxsub1 = wx.ComboBox(self, -1, "50", choices=list(map(str, list(range(1,51)))), style=wx.CB_READONLY)
self.cb_maxsub2 = wx.ComboBox(self, -1, "200", choices=list(map(str, list(range(1,201)))), style=wx.CB_READONLY)
self.ctrls.extend([self.rb_maxsub1,
self.cb_maxsub1,
self.rb_maxsub2,
self.cb_maxsub2
])
self.checkbox_stop_time = wx.CheckBox(self, -1, "Time Limit (hr)")
self.checkbox_stop_iter = wx.CheckBox(self, -1, "Iteration Limit")
self.cb_stop1 = wx.ComboBox(self, -1, "24", choices=timelimit_list, style=wx.CB_READONLY)
self._iter_limits = [1, None]
riv = RangedIntValidator(self._iter_limits[0], self._iter_limits[1])
self.text_stop2 = wx.TextCtrl(self, -1, "8", validator=riv)
# self.text_stop2.Bind(wx.EVT_KILL_FOCUS, lambda event : self.validate_iter_limit_text() and event.Skip())
# self.blindmode = wx.CheckBox(self, -1, "Blind Mode Enabled")
# self.blindmode.Value = True
self.ctrls.extend([self.checkbox_stop_time,
self.cb_stop1,
self.checkbox_stop_iter,
self.text_stop2,
])
strategy_list = ["MinCluster","Centroid", "Longest"]
self.cb_decomp = wx.ComboBox(self, -1, "MinCluster", choices=strategy_list, style=wx.CB_READONLY)
self.ctrls.append(self.cb_decomp)
self.pasta_settings_ctrl_list = []
cr = 0
# sizer.Add(wx.StaticText(self, -1, "Quick Set"), (cr, 0), flag=wx.ALIGN_LEFT )
# sizer.Add(self.cb_sate_presets, (cr, 1), flag=wx.EXPAND)
# self.pasta_settings_ctrl_list.append(self.cb_sate_presets)
cr += 1
sizer.Add(wx.StaticText(self, -1, "Max. Subproblem"), (cr,0), flag=wx.ALIGN_LEFT )
sizer.Add(self.rb_maxsub1, (cr,1), flag=wx.ALIGN_LEFT)
sizer.Add(self.cb_maxsub1, (cr,2), flag=wx.EXPAND)
self.pasta_settings_ctrl_list.extend([self.rb_maxsub1, self.cb_maxsub1])
cr += 1
sizer.Add(self.rb_maxsub2, (cr,1), flag=wx.ALIGN_LEFT)
sizer.Add(self.cb_maxsub2, (cr,2), flag=wx.EXPAND)
self.pasta_settings_ctrl_list.extend([self.rb_maxsub2, self.cb_maxsub2])
cr += 1
sizer.Add(wx.StaticText(self, -1, "Decomposition"), (cr,0), flag=wx.ALIGN_LEFT )
sizer.Add(self.cb_decomp, (cr,1), flag=wx.EXPAND)
self.pasta_settings_ctrl_list.extend([self.cb_decomp])
# cr += 1
# sizer.Add(wx.StaticText(self, -1, "Apply Stop Rule"), (cr,0), flag=wx.ALIGN_LEFT )
# sizer.Add(self.cb_apply_stop_rule, (cr,1), flag=wx.EXPAND)
# self.pasta_settings_ctrl_list.extend([self.cb_apply_stop_rule])
# cr += 1
# sizer.Add(wx.StaticText(self, -1, "Stopping Rule"), (cr,0), flag=wx.ALIGN_LEFT )
# sizer.Add(self.blindmode, (cr,1), flag=wx.EXPAND)
# self.pasta_settings_ctrl_list.extend([self.blindmode])
cr += 1
sizer.Add(self.checkbox_stop_time, (cr,1), flag=wx.ALIGN_LEFT)
sizer.Add(self.cb_stop1, (cr,2), flag=wx.EXPAND)
self.pasta_settings_ctrl_list.extend([self.checkbox_stop_time, self.cb_stop1])
cr += 1
sizer.Add(self.checkbox_stop_iter, (cr,1), flag=wx.ALIGN_LEFT)
sizer.Add(self.text_stop2, (cr,2), flag=wx.EXPAND)
self.pasta_settings_ctrl_list.extend([self.checkbox_stop_iter, self.text_stop2])
cr += 1
sizer.Add(wx.StaticText(self, -1, "Return"), (cr, 0), flag=wx.ALIGN_LEFT )
sizer.Add(self.cb_tree_and_alignment, (cr, 1), flag=wx.EXPAND)
self.pasta_settings_ctrl_list.extend([self.cb_tree_and_alignment])
self.cb_maxsub1.Disable()
self.cb_maxsub2.Disable()
self.rb_maxsub1.Value = True
self.cb_maxsub1.Enable()
self.checkbox_stop_time.Value = False
self.cb_stop1.Disable()
self.text_stop2.Enable()
self.checkbox_stop_iter.Value = True
self.text_stop2.Value = "100"
#self.Bind(wx.EVT_COMBOBOX, self.OnSatePresets, self.cb_sate_presets)
#self.OnSatePresets(self.cb_sate_presets)
#self.Bind(wx.EVT_CHECKBOX, self.OnBlindMode, self.blindmode)
self.Bind(wx.EVT_RADIOBUTTON, self.OnMaxSubproblem, self.rb_maxsub1)
self.Bind(wx.EVT_RADIOBUTTON, self.OnMaxSubproblem, self.rb_maxsub2)
self.Bind(wx.EVT_CHECKBOX, self.OnTimeRuleCheckbox, self.checkbox_stop_time)
self.Bind(wx.EVT_CHECKBOX, self.OnIterRuleCheckbox, self.checkbox_stop_iter)
self.Bind(wx.EVT_COMBOBOX, self._set_custom_pasta_settings, self.cb_decomp)
#self.Bind(wx.EVT_COMBOBOX, self._set_custom_pasta_settings, self.cb_apply_stop_rule)
self.Bind(wx.EVT_COMBOBOX, self._set_custom_pasta_settings, self.cb_stop1)
self.Bind(wx.EVT_COMBOBOX, self._set_custom_pasta_settings, self.text_stop2)
self.Bind(wx.EVT_COMBOBOX, self._set_custom_pasta_settings, self.cb_tree_and_alignment)
#cr += 1
#presets = wx.ComboBox(self, -1, "1", choices=map(str, range(1,9)), style=wx.CB_READONLY)
#sizer.Add(wx.StaticText(self, -1, "Preset Configuration"), (cr,0), flag=wx.ALIGN_LEFT )
#sizer.Add(presets, (cr,1), flag=wx.EXPAND)
staticboxsizer.Add(sizer, 0, wx.ALL, 0)
return staticboxsizer
def validate_iter_limit_text(self):
field=self.text_stop2
t = field.GetValue()
if is_valid_int_str(t, self._iter_limits[0], self._iter_limits[1]):
return True
field.SetBackgroundColour("red")
#wx.MessageBox(message='"Iteration Limit" must contain a positive integer',
# caption='Input Error', style=wx.OK|wx.ICON_ERROR)
field.SetFocus()
field.Refresh()
return False
def _create_menu(self):
self.menuBar = wx.MenuBar()
self.menuFile = wx.Menu()
self.menuHelp = wx.Menu()
self.menuFileSaveLog = self.menuFile.Append(-1, "&Save Log...\tCtrl+S")
self.menuFileExit = self.menuFile.Append(wx.ID_EXIT, "&Quit PASTA\tCtrl+Q")
self.menuHelpHelp = self.menuHelp.Append( -1, "&Help")
self.menuHelpAbout = self.menuHelp.Append(wx.ID_ABOUT, "&About PASTA")
self.menuBar.Append(self.menuFile, "&File")
self.menuBar.Append(self.menuHelp, "&Help")
self.SetMenuBar(self.menuBar)
self.Bind(wx.EVT_MENU, self.OnSaveLog, self.menuFileSaveLog)
self.Bind(wx.EVT_MENU, self.OnExit, self.menuFileExit)
self.Bind(wx.EVT_MENU, self.OnHelp, self.menuHelpHelp)
self.Bind(wx.EVT_MENU, self.OnAbout, self.menuHelpAbout)
self.Bind(wx.EVT_CLOSE, self.OnExit)
def OnTreeEstimatorChange(self, event):
self.set_char_model()
def OnDataType(self, event):
self.set_char_model()
def set_char_model(self):
if self.datatype.Value == "DNA" or self.datatype.Value == "RNA":
self.cb_tools["model"].Clear()
if self.cb_tools["treeestimator"].Value.lower() == "raxml":
self.raxml_after.Value = False
for model in self.raxml_dna_models:
self.cb_tools["model"].Append(model)
self.cb_tools["model"].SetStringSelection("GTRCAT")
elif self.cb_tools["treeestimator"].Value.lower() == "fasttree":
for model in self.fasttree_dna_models:
self.cb_tools["model"].Append(model)
self.cb_tools["model"].SetStringSelection("GTR+G20")
elif self.datatype.Value == "Protein":
self.cb_tools["model"].Clear()
if self.cb_tools["treeestimator"].Value.lower() == "raxml":
self.raxml_after.Value = False
for model in self.raxml_prot_models:
self.cb_tools["model"].Append(model)
self.cb_tools["model"].SetStringSelection("PROTCATWAGF")
elif self.cb_tools["treeestimator"].Value.lower() == "fasttree":
for model in self.fasttree_prot_models:
self.cb_tools["model"].Append(model)
self.cb_tools["model"].SetStringSelection("JTT+G20")
def OnSaveLog(self, event):
dialog = wx.FileDialog(None, "Save Log", defaultFile=self.txt_jobname.Value, wildcard = "Log files (*.log)|*.log", style=wx.FD_OVERWRITE_PROMPT|wx.FD_SAVE)
dialog.ShowModal()
fn = dialog.GetPath()
if len(fn) > 4:
if not fn[-4:] == ".log":
fn += ".log"
else:
fn += ".log"
fc = open(fn, "w")
fc.write(self.log.GetValue())
fc.close()
def OnMaxSubproblem(self, event):
self._set_custom_pasta_settings(event)
radio_selected = event.GetEventObject()
if radio_selected.GetName() == "frac":
self.cb_maxsub1.Enable()
self.cb_maxsub2.Disable()
elif radio_selected.GetName() == "size":
self.cb_maxsub2.Enable()
self.cb_maxsub1.Disable()
def OnTwoPhase(self, event):
"""
Called every time the 'Two-Phase' checkbox is clicked. The main action
that needs to occur is the Disabling/Enabling of the PASTA settings
controls
"""
if self.two_phase.Value:
for c in self.pasta_settings_ctrl_list:
c.Disable()
self.cb_tools["merger"].Disable()
self.tree_btn.Disable()
self.txt_treefn.Disable()
self.raxml_after.Disable()
else:
fragile_list = [self.cb_maxsub1, self.cb_maxsub2, self.cb_stop1, self.text_stop2]
for c in self.pasta_settings_ctrl_list:
if c not in fragile_list:
c.Enable()
if self.rb_maxsub1.Value:
self.cb_maxsub1.Enable()
else:
self.cb_maxsub2.Enable()
if self.checkbox_stop_time.Value:
self.cb_stop1.Enable()
else:
self.text_stop2.Enable()
self.cb_tools["merger"].Enable()
self.tree_btn.Enable()
self.txt_treefn.Enable()
self.raxml_after.Enable()
def OnTimeRuleCheckbox(self, event):
self._set_custom_pasta_settings(event)
if self.checkbox_stop_time.Value:
self.cb_stop1.Enable()
else:
self.cb_stop1.Disable()
def OnIterRuleCheckbox(self, event):
self._set_custom_pasta_settings(event)
if self.checkbox_stop_iter.Value:
self.text_stop2.Enable()
else:
self.text_stop2.Disable()
def OnExit(self, event):
if self.process is not None:
wx.Process.Kill(self.pid, wx.SIGKILL)
self._remove_config_file()
self.Destroy()
def OnHelp(self, event):
import wx.html
wx.FileSystem.AddHandler(wx.ZipFSHandler())
def _addBook(filename):
if not self.help.AddBook(filename, True):
wx.MessageBox("Unable to open: " + filename, "Error", wx.OK|wx.ICON_EXCLAMATION)
self.help = wx.html.HtmlHelpController(style = wx.html.HF_DEFAULT_STYLE^wx.html.HF_BOOKMARKS^wx.html.HF_INDEX)
_addBook("help.zip")
self.help.DisplayContents()
def OnAbout(self, event):
from wx.lib.wordwrap import wordwrap
info = wx.AboutDialogInfo()
info.SetName(PROGRAM_NAME)
info.SetVersion(PROGRAM_VERSION)
info.SetCopyright("Copyright (C) %s" % PROGRAM_YEAR)
info.SetWebSite((PROGRAM_WEBSITE, "%s Homepage" % PROGRAM_NAME))
info.SetLicense(PROGRAM_LICENSE)
info.SetDescription(PROGRAM_DESCRIPTION)
[info.AddDeveloper(i) for i in PROGRAM_AUTHOR]
wx.AboutBox(info)
def _show_error_dialog(self, error_msg, caption):
"""
Puts up a modal dialog with a `error_msg` and `caption`
destroys the dialog after the user clicks `OK`
"""
error_msg_dlg = wx.MessageDialog(parent=self,
message=error_msg,
caption=caption,
style=wx.OK|wx.ICON_ERROR)
error_msg_dlg.ShowModal()
error_msg_dlg.Destroy()
def OnChooseSeq(self, event):
filepath = None
parse_as_multilocus = self.cb_multilocus.Value
if not parse_as_multilocus:
dialog = wx.FileDialog(None, "Choose sequences...", wildcard = "FASTA files (*.fasta)|*.fasta|FASTA files (*.fas)|*.fas|FASTA files (*)|*", style=wx.FD_OPEN)
dialog.ShowModal()
self.txt_seqfn.SetValue( dialog.GetPath() )
filepath = self._encode_arg(self.txt_seqfn.GetValue())
if filepath and not self.txt_outputdir.GetValue():
self.txt_outputdir.SetValue(os.path.dirname(os.path.abspath(filepath)))
else:
dialog = wx.DirDialog(None, "Choose directory for multiple sequence files", style=wx.FD_OPEN)
dialog.ShowModal()
self.txt_seqfn.SetValue( dialog.GetPath() )
filepath = self._encode_arg(self.txt_seqfn.GetValue())
if PARSING_FILES_IN_GUI and filepath:
confirm_parse_dlg = wx.MessageDialog(parent=self,
message="Do you want PASTA to read the data now? (this causes PASTA to customize some of the settings for your data).",
caption="Read input data now?",
style=wx.OK|wx.CANCEL|wx.ICON_QUESTION)
result = confirm_parse_dlg.ShowModal()
confirm_parse_dlg.Destroy()
if result == wx.ID_OK:
progress_dialog = wx.ProgressDialog(title="Reading input data",
message="Parsing data files ",
maximum=100,
parent=self,
style=wx.PD_AUTO_HIDE|wx.PD_APP_MODAL)
progress_dialog.Update(1, "Beginning Parse")
error_msg = None
try:
if parse_as_multilocus:
fn_list = get_list_of_seq_filepaths_from_dir(filepath)
else:
fn_list = [filepath]
# if self.datatype.Value == "Protein":
# datatype_list = ["PROTEIN"]
# else:
datatype_list = ["DNA", "RNA", "PROTEIN"]
careful_parse = False
summary_stats = summary_stats_from_parse(fn_list,
datatype_list,
None,
careful_parse=careful_parse)
progress_dialog.Update(100, "Done")
except Exception as x:
try:
error_msg = "Problem reading the data:\n" + str(x.message)
except:
error_msg = "Unknown error encountered while reading the data."
except:
error_msg = "Unknown error encountered while reading the data."
if error_msg:
self._show_error_dialog(error_msg, caption="Input parsing error")
filepath = None
self._could_be_aligned = False
self.refresh_aligned_checkbox()
else:
read_type = summary_stats[0]
if read_type == "PROTEIN":
self.datatype.SetValue("Protein")
else:
self.datatype.SetValue(read_type)
# Set defaults from "auto_defaults"
auto_opts = get_auto_defaults_from_summary_stats(summary_stats[0], summary_stats[1], summary_stats[2])
self._could_be_aligned = summary_stats[3]
self.refresh_aligned_checkbox()
auto_pasta_opts = auto_opts["sate"]
te_str = auto_pasta_opts["tree_estimator"].upper()
self.cb_tools["treeestimator"].SetStringSelection(te_str)
self.set_char_model()
if te_str == "FASTTREE":
te_opts = auto_opts['fasttree']
self.cb_tools["model"].SetStringSelection(te_opts["GUI_model"])
self.cb_tools["merger"].SetStringSelection(auto_pasta_opts["merger"].upper())
self.cb_tools["aligner"].SetStringSelection(auto_pasta_opts["aligner"].upper())
self.cb_ncpu.SetStringSelection(str(min(MAX_NUM_CPU, auto_pasta_opts["num_cpus"])))
# Set max decomposition based on data set size (always move to actual # here)
self.rb_maxsub1.Value = False
self.cb_maxsub1.Disable()
self.rb_maxsub2.Value = True
self.cb_maxsub2.SetStringSelection(str(max(1, auto_pasta_opts["max_subproblem_size"])))
self.cb_maxsub2.Enable()
bs = auto_pasta_opts["break_strategy"]
bs = {"mincluster":"MinCluster","centroid":"Centroid", "longest":"Longest"}[bs]
#bs = bs[0].upper() + bs[1:].lower()
self.cb_decomp.SetValue(bs)
self.cb_stop1.Disable()
self.checkbox_stop_iter.Value = True
self.cb_maxsub2.SetStringSelection(str(max(1, auto_pasta_opts["max_subproblem_size"])))
self.cb_maxsub2.Enable()
if auto_pasta_opts['move_to_blind_on_worse_score']:
#self.blindmode.Value = True
t_l = auto_pasta_opts['after_blind_time_without_imp_limit']
else:
#self.blindmode.Value = False
t_l = auto_pasta_opts['time_limit']
if t_l <= 0:
self.checkbox_stop_time.Value = False
else:
self.checkbox_stop_time.Value = True
# self.cb_apply_stop_rule.SetValue("After Last Improvement")
after_blind_it_lim = auto_pasta_opts['iter_limit']
self.text_stop2.SetValue(str(after_blind_it_lim))
if self._could_be_aligned:
a_tag = "aligned"
else:
a_tag = "unaligned"
self.log.AppendText("Read %d file(s) with %s %s data. Total of %d taxa found.\n" % (len(fn_list), a_tag, read_type, summary_stats[2]))
by_file = summary_stats[1]
for n, fn in enumerate(fn_list):
t_c_tuple = by_file[n]
if self._could_be_aligned:
self.log.AppendText(' Parsing of the file "%s" returned %d sequences of length = %d\n' % (fn, t_c_tuple[0], t_c_tuple[1]))
else:
self.log.AppendText(' Parsing of the file "%s" returned %d sequences with longest length = %d\n' % (fn, t_c_tuple[0], t_c_tuple[1]))
progress_dialog.Destroy()
else:
self._could_be_aligned = True
self.refresh_aligned_checkbox()
if filepath:
if not parse_as_multilocus:
if filepath and not self.txt_outputdir.GetValue():
self.txt_outputdir.SetValue(os.path.dirname(os.path.abspath(filepath)))
else:
if filepath and not self.txt_outputdir.GetValue():
self.txt_outputdir.SetValue(os.path.abspath(filepath))
else:
self.txt_seqfn.SetValue("")
def refresh_aligned_checkbox(self):
self.checkbox_aligned.SetValue(self._could_be_aligned)
if self._could_be_aligned:
treefilename = self.txt_treefn.GetValue()
if treefilename and os.path.isfile(treefilename):
self.checkbox_aligned.Disable()
else:
self.checkbox_aligned.Enable()
else:
self.checkbox_aligned.Disable()
def OnChooseTree(self, event):
dialog = wx.FileDialog(None, "Choose tree...", wildcard = "Tree files (*.tre)|*.tre|Tree files (*.tree)|*.tree|Tree files (*.phy)|*.phy", style=wx.FD_OPEN)
dialog.ShowModal()
self.txt_treefn.SetValue( dialog.GetPath() )
self.refresh_aligned_checkbox()
def OnIdle(self, evt):
if self.process is not None:
stream = self.process.GetInputStream()
if stream is not None and stream.CanRead():
text = stream.read()
self.log.AppendText(text)
stream = self.process.GetErrorStream()
if stream is not None and stream.CanRead():
text = stream.read()
self.log.AppendText(text)
def OnProcessEnded(self, evt):
stream = self.process.GetInputStream()
if stream.CanRead():
text = stream.read()
self.log.AppendText(text)
stream = self.process.GetErrorStream()
if stream.CanRead():
text = stream.read()
self.log.AppendText(text)
self.process.Destroy()
self.process = None
self.log.AppendText("Job %s is finished.\n" % self.txt_jobname.GetValue())
self._remove_config_file()
self._ReactivateOptions()
self.statusbar.SetStatusText("PASTA Ready!")
self.button.SetLabel("Start")
def OnButton(self, event):
if self.button.GetLabel() == "Start":
self._OnStart()
elif self.button.GetLabel() == "Stop":
self._OnStop()
else:
raise ValueError("Button label %s not recognized.\n" % self.button.GetLabel() )
def OnMultiLocus(self, event):
if self.cb_multilocus.Value:
self.seq_btn.SetLabel("Sequence files ...")
else:
self.seq_btn.SetLabel("Sequence file ...")
self.txt_seqfn.SetValue("")
def _FreezeOptions(self):
self.prev_ctrls_status = []
for ctrl in self.ctrls:
self.prev_ctrls_status.append( ctrl.IsEnabled() )
ctrl.Disable()
def _ReactivateOptions(self):
for i in range(len(self.ctrls)):
self.ctrls[i].Enable(self.prev_ctrls_status[i])
def _OnStart(self):
if self.process is None:
if (not self.checkbox_stop_time.Value) and (not self.checkbox_stop_iter.Value):
self._show_error_dialog("Termination conditions are not set correctly. Either a time limit, an iteration limit, or both must be used.\n", caption="PASTA Settings Error")
return
if self.checkbox_stop_iter.Value and (not self.validate_iter_limit_text()):
self._show_error_dialog("Iteration limit is not set correctly. Enter a positive integer in that field.\n", caption="PASTA Settings Error")
return
input_filename = self._encode_arg(self.txt_seqfn.GetValue())
if not input_filename:
self._show_error_dialog("Input sequence file(s) are required.\n", caption="PASTA Settings Error")
return
if not os.path.exists(input_filename):
self._show_error_dialog('Input sequence file(s) are "%s" does not exist!.\n', caption="PASTA Settings Error")
return
if self.cb_multilocus.Value:
if not os.path.isdir(input_filename):
self._show_error_dialog('Input sequence file specification should be a directory when multilocus model is used.\n', caption="PASTA Settings Error")
return
elif not os.path.isfile(input_filename):
self._show_error_dialog('Input sequence file must be a file when single-locus mode used.\n', caption="PASTA Settings Error")
return
cfg_success = self._create_config_file()
if not cfg_success:
return
#command = [filemgr.quoted_file_path(x) for x in get_invoke_run_pasta_command()]
command = get_invoke_run_pasta_command()
treefilename = self._encode_arg(self.txt_treefn.GetValue())
jobname = self._encode_arg(self.txt_jobname.GetValue())
if not jobname:
wx.MessageBox("Job name cannot be empty, it is REQUIRED by PASTA!", "WARNING", wx.OK|wx.ICON_WARNING)
self._remove_config_file()
return
command.extend(["-i", filemgr.quoted_file_path(input_filename)])
if treefilename and os.path.isfile(treefilename):
command.extend(["-t", filemgr.quoted_file_path(treefilename)])
command.extend(["-j", filemgr.quoted_file_path(jobname) ])
if self.datatype.Value == "DNA":
dt = "dna"
elif self.datatype.Value == "RNA":
dt = "rna"
else:
dt = "protein"
command.extend(["-d", dt])
command.extend(["%s" % filemgr.quoted_file_path(self.process_cfg_file)])
if PASTA_GUI_ONLY_PRINTS_CONFIG:
self.log.AppendText("Command is:\n '%s'\n" % "' '".join(command))
self.log.AppendText("config_file:\n#############################################################\n")
for line in open(self.process_cfg_file, 'r'):
self.log.AppendText(line)
self.log.AppendText("#############################################################\n")
self._remove_config_file()
self.statusbar.SetStatusText("\n\nRun emulated!\n\n")
else:
print("running %s" %" ".join(command))
self.process = wx.Process(self)
self.process.Redirect()
self.pid = wx.Execute( " ".join(command), wx.EXEC_ASYNC, self.process)
self.button.SetLabel("Stop")
self.statusbar.SetStatusText("PASTA Running!")
self._FreezeOptions()
else:
self.log.AppendText("Job %s is still running!\n" % self.txt_jobname.GetValue())
def _OnStop(self):
if self.process is not None:
self.log.AppendText("Job %s is terminated early.\n" % self.txt_jobname.GetValue())
self.process.Kill(self.pid, wx.SIGKILL)
self._remove_config_file()
self._ReactivateOptions()
self.button.SetLabel("Start")
self.statusbar.SetStatusText("PASTA Ready!")
else:
self.log.AppendText("No active PASTA jobs to terminate!\n")
def _encode_arg(self, arg, encoding='utf-8'):
#if isinstance(arg, str):
# return arg.encode(encoding)
return arg
def _create_config_file(self):
from pasta.configure import get_configuration
cfg = get_configuration()
#if self.txt_resultdir.Value:
# basefilename = os.path.basename(self.txt_seqfn.GetValue())
# jobname = self.txt_jobname.GetValue()
# resultdir = self.txt_resultdir.Value
# cfg.commandline.output = os.path.join(resultdir, basefilename+"_%s.aln" % jobname )
# cfg.commandline.result = os.path.join(resultdir, basefilename+"_%s.tre" % jobname )
cfg.sate.aligner = self.cb_tools["aligner"].Value
cfg.sate.tree_estimator = self.cb_tools["treeestimator"].Value
if self.cb_tools["treeestimator"].Value.lower() == "raxml":
cfg.raxml.model = self.cb_tools["model"].Value
else:
model_desc = self.cb_tools["model"].Value
if model_desc == "GTR+G20":
cfg.fasttree.model = "-gtr -gamma"
elif model_desc == "GTR+CAT":
cfg.fasttree.model = "-gtr"
elif model_desc == "JC+G20":
cfg.fasttree.model = "-gamma"
elif model_desc == "JC+CAT":
cfg.fasttree.model = ""
elif model_desc == "JTT+G20":
cfg.fasttree.model = "-gamma"
elif model_desc == "JTT+CAT":
cfg.fasttree.model = ""
elif model_desc == "WAG+G20":
cfg.fasttree.model = "-wag -gamma"
elif model_desc == "WAG+CAT":
cfg.fasttree.model = "-wag"
else:
raise Exception("Unrecognized model: %s" % model_desc)
cfg.commandline.keeptemp = True
cfg.commandline.keepalignmenttemps = True
if self.checkbox_aligned.Value:
cfg.commandline.aligned = True
#cfg.commandline.untrusted = not bool(self.trusted_data.Value)
if self.cb_multilocus.Value:
cfg.commandline.multilocus = True
if self.two_phase.Value:
cfg.commandline.two_phase = True
cfg.commandline.raxml_search_after = False
else:
cfg.commandline.two_phase = False
cfg.commandline.raxml_search_after = bool(self.raxml_after.Value)
cfg.sate.merger = self.cb_tools["merger"].Value
cfg.sate.break_strategy = self.cb_decomp.Value
cfg.sate.start_tree_search_from_current = True