def OnDownload(self, e):
self.button_download.Enable(False)
words_text = self.text_box.GetValue().strip()
words_not_downloaded = list()
words = words_text.split('\n')
len_words_text = len(words_text)
if len_words_text > 0:
progressbar_frame = Progressbar(len(words))
progressbar_frame.Show(True)
for word in words:
progressbar_frame.set_label('Downloading: ' +word)
progressbar_frame.step()
try:
self.model.download(word)
except:
words_not_downloaded.append(word)
progressbar_frame.Show(False)
else:
wx.MessageBox('Enter some words', 'Info', wx.OK | wx.ICON_INFORMATION)
self.button_download.Enable(True)
self.show_completed_dialog(len(words_not_downloaded), len_words_text)
self.text_box.SetValue('\n'.join(words_not_downloaded))
def OnDownload(self, e):
self.button_download.Enable(False)
words_text = self.text_box.GetValue().strip()
words_not_downloaded = list()
words = words_text.split('\n')
len_words_text = len(words_text)
if len_words_text > 0:
progressbar_frame = Progressbar(len(words))
progressbar_frame.Show(True)
for word in words:
progressbar_frame.set_label('Downloading: ' + word)
progressbar_frame.step()
try:
self.model.download(word)
except:
words_not_downloaded.append(word)
progressbar_frame.Show(False)
else:
wx.MessageBox('Enter some words', 'Info',
wx.OK | wx.ICON_INFORMATION)
self.button_download.Enable(True)
self.show_completed_dialog(len(words_not_downloaded), len_words_text)
self.text_box.SetValue('\n'.join(words_not_downloaded))
print 'Ignoring unknown gene: %s' % rec.description
continue
if geneName in created_protein_names:
print 'Ignoring duplicate gene: %s' % rec.description
continue
# create a new Protein object
created_protein_names.add(geneName)
protein_seq[geneName] = seq
all_proteins.append(Protein(geneName, seq, params.K))
print
print "Counted k-mer (k=%d) for %d different genes (proteins)." % (
params.K, len(all_proteins))
pb = Progressbar(
'Generating frequency dictionary for k-mers that appear more than once in protein'
)
kmers_frequency = dict() # track popularity of kmer accross all proteins
i = 0
for prot in all_proteins:
i += 1
pb.update_progress(i, len(all_proteins))
for kmer in prot.repeating_non_overlapping_kmers:
if kmer not in kmers_frequency:
kmers_frequency[kmer] = set()
# add the new protein only if it's dissimilar enough from all other
# proteins that were already added and contain this kmer
protein_names = kmers_frequency[
all_prots = g1 + g2 + g3 + g4 + g5 + g6 + g7 + g8 + g9 + g10
genes = set()
genes.update(set(['HMX3', 'B7Z774', 'B4DF88', 'hCG_2039588', 'TLE3', 'BHLHE22', 'Q7KZE5', 'DKFZp762H2012', 'SP5', 'TLE4', 'TBX2', 'A0A1U9X8A2', 'PITX3', 'NKX2-3', 'B7Z4A9', 'B3KQ29', 'B4DP89', 'ZNF703', 'HOXA13', 'PBX3', 'EOMES', 'ZSWIM6', 'B7Z5Q0', 'ZIC2', 'FBXL17', 'SPTLC2', 'FOXB2', 'GSX2', 'SP8', 'Q53EU2', 'PBX1', 'FOXD3', 'IRF2BPL', 'EVX2', 'A8K350', 'Q6NW39', 'B4E2W3', 'GATA6', 'B3KUA2', 'A0A1U9X8A1', 'PBX2', 'NLK', 'B3KM67', 'NKX6-1', 'SOX21', 'RBM47', 'ID4', 'MAZ', 'FLJ20273', 'EGR2', 'RBM24', 'PRDM8', 'ZNF395']))
all_prots = list(genes)
from random import shuffle
shuffle(all_prots)
for p in all_prots:
print p
# dilute similar proteins
diluted_list = []
pb = Progressbar('Diluting proteins...')
i = 0
for protein_name1 in all_prots:
i += 1
pb.update_progress(i, len(all_prots))
redundantProt = False
for protein_name in diluted_list:
try:
#print '%s: Checking similarity of %s and %s' % (kmer, protein_name, prot.geneName)
if not utils.proteins_are_dissimilar(protein_name, protein_name1,
protein_seq[protein_name], protein_seq[protein_name1]):
redundantProt = True
break
except:
continue
if not redundantProt:
def startup(self):
"""
Construct and show the Toga application.
Usually, you would add your application to a main content box.
We then create a main window (with a name matching the app), and
show the main window.
"""
self.logger.info(
"Starting Application\n------------------------------------------------"
)
self.logger.info(str(self.paths.app))
self.facepack_dirs = set([
"African", "Asian", "Caucasian", "Central European", "EECA",
"Italmed", "MENA", "MESA", "SAMed", "Scandinavian", "Seasian",
"South American", "SpanMed", "YugoGreek"
])
self.mode_info = {
"Overwrite": "Overwrites already replaced faces",
"Preserve": "Preserves already replaced faces",
"Generate": "Generates mapping from scratch."
}
os.makedirs(str(self.paths.app) + "/.config", exist_ok=True)
if not os.path.isfile(str(self.paths.app) + "/.user/cfg.json"):
shutil.copyfile(
str(self.paths.app) + "/.user/default_cfg.json",
str(self.paths.app) + "/.user/cfg.json")
self.logger.info("Loading current profile")
self.profile_manager = Profile_Manager(
Config_Manager().get_latest_prf(
str(self.paths.app) + "/.user/cfg.json"), str(self.paths.app))
self.profile_manager.migrate_config()
self.logger.info("Creating GUI")
self.main_box = toga.Box()
self.logger.info("Created main box")
self.hook = "https://discord.com/api/webhooks/796137178328989768/ETMNtPVb-PHuZPayC5G5MZD24tdDi5jmG6jAgjZXg0FDOXjy-VIabATXPco05qLIr4ro"
# CREATE MENUBAR
troubleshooting = toga.Command(
lambda e=None, u=
"https://github.com/Maradonna90/NewGAN-Manager/wiki/Troubleshooting":
self.open_link(u),
label='Troubleshooting',
group=toga.Group.HELP,
section=1)
usage = toga.Command(
lambda e=None, u="https://www.youtube.com/watch?v=iJqZNp0nomM":
self.open_link(u),
label='User Guide',
group=toga.Group.HELP,
section=0)
faq = toga.Command(
lambda e=None, u=
"https://github.com/Maradonna90/NewGAN-Manager/wiki/FAQ": self.
open_link(u),
label='FAQ',
group=toga.Group.HELP,
section=2)
discord = toga.Command(
lambda e=None, u="https://discord.gg/UfRpJVc": self.open_link(u),
label='Discord',
group=toga.Group.HELP,
section=3)
self.commands.add(discord, faq, troubleshooting, usage)
label_width = 125
# TOP Profiles
prf_box = toga.Box()
self.logger.info("Created prf_box")
prf_inp = toga.TextInput()
self.logger.info("Created prf_inp")
self.prfsel_box = toga.Box()
prf_lab = toga.Label(text="Create Profile: ")
prf_lab.style.update(width=label_width)
prfsel_lab = toga.Label(text="Select Profile: ")
prfsel_lab.style.update(width=label_width)
self.prfsel_lst = SourceSelection(items=list(
self.profile_manager.config["Profile"].keys()),
on_select=self._set_profile_status)
self.prfsel_lst.value = self.profile_manager.cur_prf
prfsel_btn = toga.Button(
label="Delete",
on_press=lambda e=None, c=self.prfsel_lst: self._delete_profile(c))
prf_btn = toga.Button(label="Create",
on_press=lambda e=None, d=prf_inp, c=self.
prfsel_lst: self._create_profile(d, c))
self.main_box.add(prf_box)
prf_box.add(prf_lab)
prf_box.add(prf_inp)
prf_box.add(prf_btn)
prf_lab.style.update(padding_top=7)
prf_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
self.main_box.add(self.prfsel_box)
self.prfsel_box.add(prfsel_lab)
self.prfsel_box.add(self.prfsel_lst)
self.prfsel_box.add(prfsel_btn)
self.prfsel_lst.style.update(direction=ROW, padding=(0, 20), flex=1)
prfsel_lab.style.update(padding_top=7)
# MID Path selections
dir_box = toga.Box()
dir_lab = toga.Label(text="Select Image Directory: ")
dir_lab.style.update(width=label_width)
self.dir_inp = toga.TextInput(
readonly=True, initial=self.profile_manager.prf_cfg['img_dir'])
self.dir_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
self.dir_btn = toga.Button(label="...",
on_press=self.action_select_folder_dialog,
enabled=False)
rtf_box = toga.Box()
rtf_lab = toga.Label(text="RTF File: ")
rtf_lab.style.update(width=label_width)
self.rtf_inp = toga.TextInput(
readonly=True, initial=self.profile_manager.prf_cfg['rtf'])
self.rtf_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
self.rtf_btn = toga.Button(label="...",
on_press=self.action_open_file_dialog,
enabled=False)
self.main_box.add(dir_box)
self.main_box.add(rtf_box)
dir_box.add(dir_lab)
dir_box.add(self.dir_inp)
dir_box.add(self.dir_btn)
rtf_box.add(rtf_lab)
rtf_box.add(self.rtf_inp)
rtf_box.add(self.rtf_btn)
dir_lab.style.update(padding_top=7)
rtf_lab.style.update(padding_top=7)
gen_mode_box = toga.Box()
self.genmde_lab = toga.Label(text="Mode: ")
self.genmde_lab.style.update(width=label_width)
self.genmdeinfo_lab = toga.Label(text=self.mode_info["Generate"])
self.gendup = toga.Switch(label="Allow Duplicates?")
self.genmde_lst = SourceSelection(items=list(self.mode_info.keys()),
on_select=self.update_label)
self.genmde_lst.value = "Generate"
self.genmde_lst.style.update(direction=ROW, padding=(0, 20), flex=1)
self.genmde_lab.style.update(padding_top=7)
self.genmdeinfo_lab.style.update(padding_top=7)
self.gendup.style.update(padding_top=7, padding_left=20)
gen_mode_box.add(self.genmde_lab)
gen_mode_box.add(self.genmde_lst)
gen_mode_box.add(self.genmdeinfo_lab)
gen_mode_box.add(self.gendup)
self.main_box.add(gen_mode_box)
# BOTTOM Generation
gen_box = toga.Box()
self.gen_btn = toga.Button(label="Replace Faces",
on_press=self._replace_faces,
enabled=False)
self.gen_btn.style.update(padding_bottom=20)
self.gen_lab = toga.Label(text="")
# self.gen_prg = toga.ProgressBar(max=110)
self.gen_prg = Progressbar(label=self.gen_lab)
gen_box.add(self.gen_btn)
gen_box.add(self.gen_lab)
gen_box.add(self.gen_prg)
self.main_box.add(gen_box)
self.gen_prg.style.update(width=570, alignment="center")
self.gen_lab.style.update(padding_top=20,
padding_bottom=20,
width=100,
alignment="center")
# Report bad image
rep_box = toga.Box()
self.rep_lab = toga.Label(text="Player UID: ")
self.rep_lab.style.update(width=label_width)
self.rep_inp = toga.TextInput(on_change=self.change_image)
self.rep_img = toga.ImageView(toga.Image("resources/logo.png"))
self.rep_img.style.update(height=180)
self.rep_img.style.update(width=180)
self.rep_btn = toga.Button(label="Report",
on_press=self.send_report,
enabled=False)
rep_box.add(self.rep_lab)
rep_box.add(self.rep_inp)
rep_box.add(self.rep_img)
rep_box.add(self.rep_btn)
self.main_box.add(rep_box)
self.rep_lab.style.update(padding_top=10)
self.rep_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
# END config
self.prfsel_box.style.update(padding_bottom=20)
dir_box.style.update(padding_bottom=20)
prf_box.style.update(padding_bottom=20)
rtf_box.style.update(padding_bottom=20)
gen_mode_box.style.update(padding_bottom=20)
rep_box.style.update(padding_top=20)
gen_box.style.update(direction=COLUMN, alignment='center')
self.main_box.style.update(direction=COLUMN,
padding=30,
alignment='center')
self.main_window = toga.MainWindow(title=self.formal_name,
size=(1000, 600))
self.main_window.content = self.main_box
self.main_window.show()
self.check_for_update()
class NewGANManager(toga.App):
def __init__(self, log):
super().__init__()
self.logger = log
def startup(self):
"""
Construct and show the Toga application.
Usually, you would add your application to a main content box.
We then create a main window (with a name matching the app), and
show the main window.
"""
self.logger.info(
"Starting Application\n------------------------------------------------"
)
self.logger.info(str(self.paths.app))
self.facepack_dirs = set([
"African", "Asian", "Caucasian", "Central European", "EECA",
"Italmed", "MENA", "MESA", "SAMed", "Scandinavian", "Seasian",
"South American", "SpanMed", "YugoGreek"
])
self.mode_info = {
"Overwrite": "Overwrites already replaced faces",
"Preserve": "Preserves already replaced faces",
"Generate": "Generates mapping from scratch."
}
os.makedirs(str(self.paths.app) + "/.config", exist_ok=True)
if not os.path.isfile(str(self.paths.app) + "/.user/cfg.json"):
shutil.copyfile(
str(self.paths.app) + "/.user/default_cfg.json",
str(self.paths.app) + "/.user/cfg.json")
self.logger.info("Loading current profile")
self.profile_manager = Profile_Manager(
Config_Manager().get_latest_prf(
str(self.paths.app) + "/.user/cfg.json"), str(self.paths.app))
self.profile_manager.migrate_config()
self.logger.info("Creating GUI")
self.main_box = toga.Box()
self.logger.info("Created main box")
self.hook = "https://discord.com/api/webhooks/796137178328989768/ETMNtPVb-PHuZPayC5G5MZD24tdDi5jmG6jAgjZXg0FDOXjy-VIabATXPco05qLIr4ro"
# CREATE MENUBAR
troubleshooting = toga.Command(
lambda e=None, u=
"https://github.com/Maradonna90/NewGAN-Manager/wiki/Troubleshooting":
self.open_link(u),
label='Troubleshooting',
group=toga.Group.HELP,
section=1)
usage = toga.Command(
lambda e=None, u="https://www.youtube.com/watch?v=iJqZNp0nomM":
self.open_link(u),
label='User Guide',
group=toga.Group.HELP,
section=0)
faq = toga.Command(
lambda e=None, u=
"https://github.com/Maradonna90/NewGAN-Manager/wiki/FAQ": self.
open_link(u),
label='FAQ',
group=toga.Group.HELP,
section=2)
discord = toga.Command(
lambda e=None, u="https://discord.gg/UfRpJVc": self.open_link(u),
label='Discord',
group=toga.Group.HELP,
section=3)
self.commands.add(discord, faq, troubleshooting, usage)
label_width = 125
# TOP Profiles
prf_box = toga.Box()
self.logger.info("Created prf_box")
prf_inp = toga.TextInput()
self.logger.info("Created prf_inp")
self.prfsel_box = toga.Box()
prf_lab = toga.Label(text="Create Profile: ")
prf_lab.style.update(width=label_width)
prfsel_lab = toga.Label(text="Select Profile: ")
prfsel_lab.style.update(width=label_width)
self.prfsel_lst = SourceSelection(items=list(
self.profile_manager.config["Profile"].keys()),
on_select=self._set_profile_status)
self.prfsel_lst.value = self.profile_manager.cur_prf
prfsel_btn = toga.Button(
label="Delete",
on_press=lambda e=None, c=self.prfsel_lst: self._delete_profile(c))
prf_btn = toga.Button(label="Create",
on_press=lambda e=None, d=prf_inp, c=self.
prfsel_lst: self._create_profile(d, c))
self.main_box.add(prf_box)
prf_box.add(prf_lab)
prf_box.add(prf_inp)
prf_box.add(prf_btn)
prf_lab.style.update(padding_top=7)
prf_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
self.main_box.add(self.prfsel_box)
self.prfsel_box.add(prfsel_lab)
self.prfsel_box.add(self.prfsel_lst)
self.prfsel_box.add(prfsel_btn)
self.prfsel_lst.style.update(direction=ROW, padding=(0, 20), flex=1)
prfsel_lab.style.update(padding_top=7)
# MID Path selections
dir_box = toga.Box()
dir_lab = toga.Label(text="Select Image Directory: ")
dir_lab.style.update(width=label_width)
self.dir_inp = toga.TextInput(
readonly=True, initial=self.profile_manager.prf_cfg['img_dir'])
self.dir_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
self.dir_btn = toga.Button(label="...",
on_press=self.action_select_folder_dialog,
enabled=False)
rtf_box = toga.Box()
rtf_lab = toga.Label(text="RTF File: ")
rtf_lab.style.update(width=label_width)
self.rtf_inp = toga.TextInput(
readonly=True, initial=self.profile_manager.prf_cfg['rtf'])
self.rtf_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
self.rtf_btn = toga.Button(label="...",
on_press=self.action_open_file_dialog,
enabled=False)
self.main_box.add(dir_box)
self.main_box.add(rtf_box)
dir_box.add(dir_lab)
dir_box.add(self.dir_inp)
dir_box.add(self.dir_btn)
rtf_box.add(rtf_lab)
rtf_box.add(self.rtf_inp)
rtf_box.add(self.rtf_btn)
dir_lab.style.update(padding_top=7)
rtf_lab.style.update(padding_top=7)
gen_mode_box = toga.Box()
self.genmde_lab = toga.Label(text="Mode: ")
self.genmde_lab.style.update(width=label_width)
self.genmdeinfo_lab = toga.Label(text=self.mode_info["Generate"])
self.gendup = toga.Switch(label="Allow Duplicates?")
self.genmde_lst = SourceSelection(items=list(self.mode_info.keys()),
on_select=self.update_label)
self.genmde_lst.value = "Generate"
self.genmde_lst.style.update(direction=ROW, padding=(0, 20), flex=1)
self.genmde_lab.style.update(padding_top=7)
self.genmdeinfo_lab.style.update(padding_top=7)
self.gendup.style.update(padding_top=7, padding_left=20)
gen_mode_box.add(self.genmde_lab)
gen_mode_box.add(self.genmde_lst)
gen_mode_box.add(self.genmdeinfo_lab)
gen_mode_box.add(self.gendup)
self.main_box.add(gen_mode_box)
# BOTTOM Generation
gen_box = toga.Box()
self.gen_btn = toga.Button(label="Replace Faces",
on_press=self._replace_faces,
enabled=False)
self.gen_btn.style.update(padding_bottom=20)
self.gen_lab = toga.Label(text="")
# self.gen_prg = toga.ProgressBar(max=110)
self.gen_prg = Progressbar(label=self.gen_lab)
gen_box.add(self.gen_btn)
gen_box.add(self.gen_lab)
gen_box.add(self.gen_prg)
self.main_box.add(gen_box)
self.gen_prg.style.update(width=570, alignment="center")
self.gen_lab.style.update(padding_top=20,
padding_bottom=20,
width=100,
alignment="center")
# Report bad image
rep_box = toga.Box()
self.rep_lab = toga.Label(text="Player UID: ")
self.rep_lab.style.update(width=label_width)
self.rep_inp = toga.TextInput(on_change=self.change_image)
self.rep_img = toga.ImageView(toga.Image("resources/logo.png"))
self.rep_img.style.update(height=180)
self.rep_img.style.update(width=180)
self.rep_btn = toga.Button(label="Report",
on_press=self.send_report,
enabled=False)
rep_box.add(self.rep_lab)
rep_box.add(self.rep_inp)
rep_box.add(self.rep_img)
rep_box.add(self.rep_btn)
self.main_box.add(rep_box)
self.rep_lab.style.update(padding_top=10)
self.rep_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
# END config
self.prfsel_box.style.update(padding_bottom=20)
dir_box.style.update(padding_bottom=20)
prf_box.style.update(padding_bottom=20)
rtf_box.style.update(padding_bottom=20)
gen_mode_box.style.update(padding_bottom=20)
rep_box.style.update(padding_top=20)
gen_box.style.update(direction=COLUMN, alignment='center')
self.main_box.style.update(direction=COLUMN,
padding=30,
alignment='center')
self.main_window = toga.MainWindow(title=self.formal_name,
size=(1000, 600))
self.main_window.content = self.main_box
self.main_window.show()
self.check_for_update()
def open_link(self, url):
webbrowser.open(url)
def update_label(self, widget):
self.logger.info("Updating generation label")
self.genmdeinfo_lab.text = self.mode_info[widget.value]
def set_btns(self, value):
if self.profile_manager.cur_prf == "No Profile":
self.gen_btn.enabled = False
self.dir_btn.enabled = False
self.rtf_btn.enabled = False
self.rep_btn.enabled = False
else:
self.gen_btn.enabled = value
self.dir_btn.enabled = value
self.rtf_btn.enabled = value
self.rep_btn.enabled = value
def _set_profile_status(self, e):
self.logger.info("switch profile: {}".format(e.value))
if e.value is None:
self.logger.info("catch none {}".format(
self.profile_manager.cur_prf))
elif e.value == self.profile_manager.cur_prf:
self.logger.info("catch same values")
else:
name = e.value
self.profile_manager.load_profile(name)
self._refresh_inp()
self.set_btns(True)
Config_Manager().save_config(
str(self.paths.app) + "/.user/cfg.json",
self.profile_manager.config)
def _refresh_inp(self, clear=False):
self.logger.info("Refresh Input Buttons")
if clear:
self.dir_inp.clear()
self.rtf_inp.clear()
else:
self.dir_inp.value = self.profile_manager.prf_cfg['img_dir']
self.rtf_inp.value = self.profile_manager.prf_cfg['rtf']
def _create_profile(self, ent, c):
name = ent.value
self.profile_manager.create_profile(name)
ent.clear()
c.add_item(name)
def _delete_profile(self, c):
prf = c.value
self.profile_manager.delete_profile(prf)
c.remove_item(prf)
self._refresh_inp(True)
self.set_btns(False)
def _throw_error(self, msg):
self.logger.info("Error window {}:".format(msg))
self.main_window.error_dialog('Error', msg)
def _show_info(self, msg):
self.logger.info("Info window: {}".format(msg))
self.main_window.info_dialog("Info", msg)
def action_select_folder_dialog(self, widget):
self.logger.info("Select Folder...")
try:
path_names = self.main_window.select_folder_dialog(
title="Select image root folder")
self.dir_inp.value = path_names[0] + "/"
self.profile_manager.prf_cfg['img_dir'] = path_names[0] + "/"
Config_Manager().save_config(
str(self.paths.app) + "/.user/" +
self.profile_manager.cur_prf + ".json",
self.profile_manager.prf_cfg)
except Exception:
pass
def action_open_file_dialog(self, widget):
self.logger.info("Select File...")
try:
fname = self.main_window.open_file_dialog(title="Open RTF file",
multiselect=False,
file_types=['rtf'])
self.logger.info("Created file-dialog")
if fname is not None:
fname = str(fname)
self.rtf_inp.value = fname
self.profile_manager.prf_cfg['rtf'] = fname
self.logger.info("RTF file: " + fname)
Config_Manager().save_config(
str(self.paths.app) + "/.user/" +
self.profile_manager.cur_prf + ".json",
self.profile_manager.prf_cfg)
else:
self.profile_manager.prf_cfg['rtf'] = ""
self.rtf_inp.value = ""
Config_Manager().save_config(
str(self.paths.app) + "/.user/" +
self.profile_manager.cur_prf + ".json",
self.profile_manager.prf_cfg)
except Exception:
self.logger.error("Fatal error in main loop", exc_info=True)
pass
def _replace_faces(self, widget):
self.logger.info("Start Replace Faces")
# get values from UI elements
rtf = self.profile_manager.prf_cfg['rtf']
img_dir = self.profile_manager.prf_cfg['img_dir']
profile = self.profile_manager.cur_prf
mode = self.genmde_lst.value
if not os.path.isfile(rtf):
self._throw_error("The RTF file doesn't exist!")
self.gen_prg.stop()
self.profile_manager.prf_cfg['rtf'] = ''
return
if not os.path.isdir(img_dir):
self._throw_error("The image directory doesn't exist!")
self.gen_prg.stop()
self.profile_manager.prf_cfg['img_dir'] = ''
return
# Check if valid image_directory contains all the needed subfolders
img_dirs = set()
for entry in os.scandir(img_dir):
if entry.is_dir():
img_dirs.add(entry.name)
for fp_dir in self.facepack_dirs:
if fp_dir not in img_dirs:
self._throw_error(
"Folder {} is missing in the image directory".format(
fp_dir))
self.gen_prg.stop()
return
self.logger.info("rtf: {}".format(rtf))
self.logger.info("img_dir: {}".format(img_dir))
self.logger.info("profile: {}".format(profile))
self.logger.info("mode: {}".format(mode))
self.set_btns(False)
self.gen_prg.start()
self.gen_prg.update_label("Parsing RTF")
# yield 0.1
rtf_parser = RTF_Parser()
if not rtf_parser.is_rtf_valid(rtf):
self._throw_error("The RTF file is invalid!")
self.gen_prg.stop()
return
rtf_data = rtf_parser.parse_rtf(rtf)
self.gen_prg.update_progress(20)
self.gen_prg.update_label("Map player to ethnicity")
# yield 0.1
mapping_data = Mapper(img_dir, self.profile_manager).generate_mapping(
rtf_data, mode, self.gendup.is_on)
self.gen_prg.update_progress(60)
self.gen_prg.update_label("Generate config.xml")
# yield 0.1
self.profile_manager.write_xml(mapping_data)
# save profile metadata (used pics and config.xml)
self.gen_prg.update_label("Save metadata for profile")
self.gen_prg.update_progress(10)
# yield 0.1
Config_Manager().save_config(
str(self.paths.app) + "/.user/" + profile + ".json",
self.profile_manager.prf_cfg)
self.gen_prg.update_progress(10)
# yield 0.1
self.gen_prg.update_label("Finished! :)")
# yield 0.1
self._show_info("Finished! :)")
self.gen_prg.stop()
self.set_btns(True)
def change_image(self, id):
self.logger.info("try to change image preview")
uid = id.value
if len(uid) >= 7:
try:
img_path = XML_Parser().get_imgpath_from_uid(
self.profile_manager.prf_cfg['img_dir'] + "config.xml",
uid)
img_path = self.profile_manager.prf_cfg[
'img_dir'] + img_path + ".png"
self.rep_img.image = toga.Image(img_path)
self.logger.info(
"change image preview to: {}".format(img_path))
except Exception as e:
self.logger.info("changing image preview failed!")
self.logger.info(e)
return
return
def send_report(self, e):
uid = self.rep_inp.value
if len(uid) >= 7:
rep = Reporter(
self.hook,
self.profile_manager.prf_cfg['img_dir'] + "config.xml")
res = rep.send_report(uid)
if res:
self._show_info("Thanks for Reporting!")
self.rep_img.image = toga.Image("resources/logo.png")
self.rep_inp.value = ""
else:
self._throw_error(
"Player with ID {} doesn't exist!".format(uid))
self.rep_img.image = toga.Image("resources/logo.png")
self.rep_inp.value = ""
def check_for_update(self):
r = requests.get(
"https://raw.githubusercontent.com/Maradonna90/NewGAN-Manager/master/version"
)
if r.text.strip() != self.version:
self._show_info("There is a new version. Please Update!")
self.open_link(
"https://github.com/Maradonna90/NewGAN-Manager/releases/latest"
)
def main(proteome_file, similar_diluted):
all_proteins = list() # all_proteins[i] = PROTEIN()_OBJECT
protein_seq = dict() # protein_seq[GENE_NAME] = AMINO_ACID_SEQUENCE
print "Reading Uniprot file and generating k-mers list for each protein..."
created_protein_names = set(
) # prevent creation of two similar protein objects
duplicate_genes_ignored = 0
for rec in SeqIO.parse(open(proteome_file), 'fasta'):
seq = str(rec.seq)
uniqueIdentifier, entryName, proteinName, organismName, geneName = \
utils.parse_UniProtKB_header(rec.description)
if geneName == '':
geneName = uniqueIdentifier
#print 'Using uncharacterized gene with identifier %s' % uniqueIdentifier
#print 'Ignoring unknown gene: %s' % rec.description
#continue
if geneName in created_protein_names:
duplicate_genes_ignored += 1
#print 'Ignoring duplicate gene: %s' % rec.description
continue
# create a new Protein object
created_protein_names.add(geneName)
protein_seq[geneName] = seq
all_proteins.append(Protein(geneName, seq, params.K))
print
print "Ignored %d duplicate genes." % duplicate_genes_ignored
print "Counted k-mer (k=%d) for %d different genes (proteins)." % (
params.K, len(all_proteins))
pb = Progressbar('Generating frequency dictionary for k-mers')
kmers_frequency = dict() # track popularity of kmer accross all proteins
i = 0
for prot in all_proteins:
i += 1
pb.update_progress(i, len(all_proteins))
for kmer in prot.kmers:
if kmer not in kmers_frequency:
kmers_frequency[kmer] = set()
# add the new protein only if it's dissimilar enough from all other
# proteins that were already added and contain this kmer
protein_names = kmers_frequency[
kmer] # list of all prots that share this kmer
redundantProt = False
if similar_diluted:
for protein_name in protein_names:
#print '%s: Checking similarity of %s and %s' % (kmer, protein_name, prot.geneName)
if not utils.proteins_are_dissimilar(
protein_name, prot.geneName,
protein_seq[protein_name], prot.seq):
redundantProt = True
break
if not redundantProt:
kmers_frequency[kmer].add(prot.geneName)
redundantProt = False
print "Sorting frequent k-mers by frequency..."
most_frequenct_kmers = sorted(kmers_frequency,
key=lambda k: len(kmers_frequency[k]),
reverse=True)
print "Writing results to file..."
import datetime, time, csv
timestamp = datetime.datetime.fromtimestamp(
time.time()).strftime('%Y-%m-%d-%H%M%S')
filename_without_extension = os.path.splitext(
os.path.basename(proteome_file))[0]
dilution_status = 'with dilution' if similar_diluted else 'without dilution'
outfile = "{0} - frequent k{1}-mers - {2} - {3}.csv".format(
filename_without_extension, params.K, dilution_status, timestamp)
outfile = os.path.join(os.path.dirname(proteome_file), outfile)
with open(outfile, "wb") as csv_file:
writer = csv.writer(csv_file, delimiter=',')
writer.writerow([
'k-mer', 'number of proteins', 'percentage', 'all',
'(Out of %d proteins in total)' % len(all_proteins)
])
for kmer in most_frequenct_kmers:
total_proteins = len(kmers_frequency[kmer])
if total_proteins < 5:
break
percentage = round(float(total_proteins) / len(all_proteins), 6)
geneList = list(kmers_frequency[kmer])
#geneList = '\r\n'.join(geneList)
row = [kmer, total_proteins, percentage, geneList]
writer.writerow(row)
def startup(self):
"""
Construct and show the Toga application.
Usually, you would add your application to a main content box.
We then create a main window (with a name matching the app), and
show the main window.
"""
self.logger.info(
"Starting Application\n------------------------------------------------"
)
self.logger.info(str(self.paths.app))
self.mode_info = {
"Overwrite": "Overwrites already replaced faces",
"Preserve": "Preserves already replaced faces",
"Generate": "Generates mapping from scratch."
}
os.makedirs(str(self.paths.app) + "/.config", exist_ok=True)
self.logger.info("Loading current profile")
self.profile_manager = Profile_Manager(
Config_Manager().get_latest_prf(
str(self.paths.app) + "/.user/cfg.json"), str(self.paths.app))
self.profile_manager.migrate_config()
self.logger.info("Creating GUI")
self.main_box = toga.Box()
self.logger.info("Created main box")
label_width = 125
# TOP Profiles
prf_box = toga.Box()
self.logger.info("Created prf_box")
prf_inp = toga.TextInput()
self.logger.info("Created prf_inp")
self.prfsel_box = toga.Box()
prf_lab = toga.Label(text="Create Profile: ")
prf_lab.style.update(width=label_width)
prfsel_lab = toga.Label(text="Select Profile: ")
prfsel_lab.style.update(width=label_width)
self.prfsel_lst = SourceSelection(items=list(
self.profile_manager.config["Profile"].keys()),
on_select=self._set_profile_status)
self.prfsel_lst.value = self.profile_manager.cur_prf
prfsel_btn = toga.Button(
label="Delete",
on_press=lambda e=None, c=self.prfsel_lst: self._delete_profile(c))
prf_btn = toga.Button(label="Create",
on_press=lambda e=None, d=prf_inp, c=self.
prfsel_lst: self._create_profile(d, c))
self.main_box.add(prf_box)
prf_box.add(prf_lab)
prf_box.add(prf_inp)
prf_box.add(prf_btn)
prf_lab.style.update(padding_top=7)
prf_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
self.main_box.add(self.prfsel_box)
self.prfsel_box.add(prfsel_lab)
self.prfsel_box.add(self.prfsel_lst)
self.prfsel_box.add(prfsel_btn)
self.prfsel_lst.style.update(direction=ROW, padding=(0, 20), flex=1)
prfsel_lab.style.update(padding_top=7)
# MID Path selections
dir_box = toga.Box()
dir_lab = toga.Label(text="Select Image Directory: ")
dir_lab.style.update(width=label_width)
self.dir_inp = toga.TextInput(
readonly=True, initial=self.profile_manager.prf_cfg['img_dir'])
self.dir_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
self.dir_btn = toga.Button(label="...",
on_press=self.action_select_folder_dialog,
enabled=False)
rtf_box = toga.Box()
rtf_lab = toga.Label(text="RTF File: ")
rtf_lab.style.update(width=label_width)
self.rtf_inp = toga.TextInput(
readonly=True, initial=self.profile_manager.prf_cfg['rtf'])
self.rtf_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
self.rtf_btn = toga.Button(label="...",
on_press=self.action_open_file_dialog,
enabled=False)
self.main_box.add(dir_box)
self.main_box.add(rtf_box)
dir_box.add(dir_lab)
dir_box.add(self.dir_inp)
dir_box.add(self.dir_btn)
rtf_box.add(rtf_lab)
rtf_box.add(self.rtf_inp)
rtf_box.add(self.rtf_btn)
dir_lab.style.update(padding_top=7)
rtf_lab.style.update(padding_top=7)
gen_mode_box = toga.Box()
self.genmde_lab = toga.Label(text="Mode: ")
self.genmde_lab.style.update(width=label_width)
self.genmdeinfo_lab = toga.Label(text=self.mode_info["Generate"])
self.genmde_lst = SourceSelection(items=list(self.mode_info.keys()),
on_select=self.update_label)
self.genmde_lst.value = "Generate"
self.genmde_lst.style.update(direction=ROW, padding=(0, 20), flex=1)
self.genmde_lab.style.update(padding_top=7)
self.genmdeinfo_lab.style.update(padding_top=7)
gen_mode_box.add(self.genmde_lab)
gen_mode_box.add(self.genmde_lst)
gen_mode_box.add(self.genmdeinfo_lab)
self.main_box.add(gen_mode_box)
# BOTTOM Generation
gen_box = toga.Box()
self.gen_btn = toga.Button(label="Replace Faces",
on_press=self._replace_faces,
enabled=False)
self.gen_btn.style.update(padding_bottom=20)
self.gen_lab = toga.Label(text="")
# self.gen_prg = toga.ProgressBar(max=110)
self.gen_prg = Progressbar(label=self.gen_lab)
gen_box.add(self.gen_btn)
gen_box.add(self.gen_lab)
gen_box.add(self.gen_prg)
self.main_box.add(gen_box)
self.gen_prg.style.update(width=570, alignment="center")
self.gen_lab.style.update(padding_top=20,
padding_bottom=20,
width=100,
alignment="center")
# Report bad image
rep_box = toga.Box()
self.rep_lab = toga.Label(text="Player UID: ")
self.rep_lab.style.update(width=label_width)
self.rep_inp = toga.TextInput(on_change=self.change_image)
self.rep_img = toga.ImageView(toga.Image("resources/logo.png"))
self.rep_img.style.update(height=180)
self.rep_img.style.update(width=180)
self.rep_btn = toga.Button(label="Report",
on_press=self.send_report,
enabled=False)
rep_box.add(self.rep_lab)
rep_box.add(self.rep_inp)
rep_box.add(self.rep_img)
rep_box.add(self.rep_btn)
self.main_box.add(rep_box)
self.rep_lab.style.update(padding_top=10)
self.rep_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
# END config
self.prfsel_box.style.update(padding_bottom=20)
dir_box.style.update(padding_bottom=20)
prf_box.style.update(padding_bottom=20)
rtf_box.style.update(padding_bottom=20)
gen_mode_box.style.update(padding_bottom=20)
rep_box.style.update(padding_top=20)
gen_box.style.update(direction=COLUMN, alignment='center')
self.main_box.style.update(direction=COLUMN,
padding=30,
alignment='center')
self.main_window = toga.MainWindow(title=self.formal_name,
size=(1000, 600))
self.main_window.content = self.main_box
self.main_window.show()
# ORIGINAL_DATASET_PATH = 'dataset/recent_tweets_test/houston_tweets.csv'
# PROCESSED_DATASET_PATH = 'dataset/recent_tweets_test/houston_tweets-extended.csv'
ORIGINAL_DATASET_PATH = 'dataset/recent_tweets_test/miami_tweets.csv'
PROCESSED_DATASET_PATH = 'dataset/recent_tweets_test/miami_tweets-extended.csv'
# Read original dataset
logger.info('Reading from %s' % ORIGINAL_DATASET_PATH)
orig_dataset = [
tweetRec for tweetRec in csv.DictReader(open(ORIGINAL_DATASET_PATH, 'rb'))
]
total_tweets = len(orig_dataset)
logger.info('%d rows fetched' % total_tweets)
# Write new dataset
logger.info('Writing to %s' % PROCESSED_DATASET_PATH)
pb = Progressbar('Building extended dataset')
with open(PROCESSED_DATASET_PATH, 'wb') as csvfile:
dataset_keys = orig_dataset[0].keys() + ['link_url1', 'link_uri1', 'link_title1',\
'link_url2', 'link_uri2', 'link_title2',\
'link_url3', 'link_uri3', 'link_title3']
csvwriter = csv.DictWriter(csvfile, fieldnames=dataset_keys)
csvwriter.writeheader()
for i in xrange(len(orig_dataset)):
pb.update_progress(i, total_tweets)
tweet = orig_dataset[i]['text']
try:
# Step 1 - Check if there are any links in tweet
tweet_parser = ttp.Parser().parse(tweet)
class NewGANManager(toga.App):
def __init__(self, log):
super().__init__()
self.logger = log
def startup(self):
"""
Construct and show the Toga application.
Usually, you would add your application to a main content box.
We then create a main window (with a name matching the app), and
show the main window.
"""
self.logger.info(
"Starting Application\n------------------------------------------------"
)
self.logger.info(str(self.paths.app))
self.mode_info = {
"Overwrite": "Overwrites already replaced faces",
"Preserve": "Preserves already replaced faces",
"Generate": "Generates mapping from scratch."
}
os.makedirs(str(self.paths.app) + "/.config", exist_ok=True)
self.logger.info("Loading current profile")
self.profile_manager = Profile_Manager(
Config_Manager().get_latest_prf(
str(self.paths.app) + "/.user/cfg.json"), str(self.paths.app))
self.profile_manager.migrate_config()
self.logger.info("Creating GUI")
self.main_box = toga.Box()
self.logger.info("Created main box")
label_width = 125
# TOP Profiles
prf_box = toga.Box()
self.logger.info("Created prf_box")
prf_inp = toga.TextInput()
self.logger.info("Created prf_inp")
self.prfsel_box = toga.Box()
prf_lab = toga.Label(text="Create Profile: ")
prf_lab.style.update(width=label_width)
prfsel_lab = toga.Label(text="Select Profile: ")
prfsel_lab.style.update(width=label_width)
self.prfsel_lst = SourceSelection(items=list(
self.profile_manager.config["Profile"].keys()),
on_select=self._set_profile_status)
self.prfsel_lst.value = self.profile_manager.cur_prf
prfsel_btn = toga.Button(
label="Delete",
on_press=lambda e=None, c=self.prfsel_lst: self._delete_profile(c))
prf_btn = toga.Button(label="Create",
on_press=lambda e=None, d=prf_inp, c=self.
prfsel_lst: self._create_profile(d, c))
self.main_box.add(prf_box)
prf_box.add(prf_lab)
prf_box.add(prf_inp)
prf_box.add(prf_btn)
prf_lab.style.update(padding_top=7)
prf_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
self.main_box.add(self.prfsel_box)
self.prfsel_box.add(prfsel_lab)
self.prfsel_box.add(self.prfsel_lst)
self.prfsel_box.add(prfsel_btn)
self.prfsel_lst.style.update(direction=ROW, padding=(0, 20), flex=1)
prfsel_lab.style.update(padding_top=7)
# MID Path selections
dir_box = toga.Box()
dir_lab = toga.Label(text="Select Image Directory: ")
dir_lab.style.update(width=label_width)
self.dir_inp = toga.TextInput(
readonly=True, initial=self.profile_manager.prf_cfg['img_dir'])
self.dir_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
self.dir_btn = toga.Button(label="...",
on_press=self.action_select_folder_dialog,
enabled=False)
rtf_box = toga.Box()
rtf_lab = toga.Label(text="RTF File: ")
rtf_lab.style.update(width=label_width)
self.rtf_inp = toga.TextInput(
readonly=True, initial=self.profile_manager.prf_cfg['rtf'])
self.rtf_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
self.rtf_btn = toga.Button(label="...",
on_press=self.action_open_file_dialog,
enabled=False)
self.main_box.add(dir_box)
self.main_box.add(rtf_box)
dir_box.add(dir_lab)
dir_box.add(self.dir_inp)
dir_box.add(self.dir_btn)
rtf_box.add(rtf_lab)
rtf_box.add(self.rtf_inp)
rtf_box.add(self.rtf_btn)
dir_lab.style.update(padding_top=7)
rtf_lab.style.update(padding_top=7)
gen_mode_box = toga.Box()
self.genmde_lab = toga.Label(text="Mode: ")
self.genmde_lab.style.update(width=label_width)
self.genmdeinfo_lab = toga.Label(text=self.mode_info["Generate"])
self.genmde_lst = SourceSelection(items=list(self.mode_info.keys()),
on_select=self.update_label)
self.genmde_lst.value = "Generate"
self.genmde_lst.style.update(direction=ROW, padding=(0, 20), flex=1)
self.genmde_lab.style.update(padding_top=7)
self.genmdeinfo_lab.style.update(padding_top=7)
gen_mode_box.add(self.genmde_lab)
gen_mode_box.add(self.genmde_lst)
gen_mode_box.add(self.genmdeinfo_lab)
self.main_box.add(gen_mode_box)
# BOTTOM Generation
gen_box = toga.Box()
self.gen_btn = toga.Button(label="Replace Faces",
on_press=self._replace_faces,
enabled=False)
self.gen_btn.style.update(padding_bottom=20)
self.gen_lab = toga.Label(text="")
# self.gen_prg = toga.ProgressBar(max=110)
self.gen_prg = Progressbar(label=self.gen_lab)
gen_box.add(self.gen_btn)
gen_box.add(self.gen_lab)
gen_box.add(self.gen_prg)
self.main_box.add(gen_box)
self.gen_prg.style.update(width=570, alignment="center")
self.gen_lab.style.update(padding_top=20,
padding_bottom=20,
width=100,
alignment="center")
# Report bad image
rep_box = toga.Box()
self.rep_lab = toga.Label(text="Player UID: ")
self.rep_lab.style.update(width=label_width)
self.rep_inp = toga.TextInput(on_change=self.change_image)
self.rep_img = toga.ImageView(toga.Image("resources/logo.png"))
self.rep_img.style.update(height=180)
self.rep_img.style.update(width=180)
self.rep_btn = toga.Button(label="Report",
on_press=self.send_report,
enabled=False)
rep_box.add(self.rep_lab)
rep_box.add(self.rep_inp)
rep_box.add(self.rep_img)
rep_box.add(self.rep_btn)
self.main_box.add(rep_box)
self.rep_lab.style.update(padding_top=10)
self.rep_inp.style.update(direction=ROW, padding=(0, 20), flex=1)
# END config
self.prfsel_box.style.update(padding_bottom=20)
dir_box.style.update(padding_bottom=20)
prf_box.style.update(padding_bottom=20)
rtf_box.style.update(padding_bottom=20)
gen_mode_box.style.update(padding_bottom=20)
rep_box.style.update(padding_top=20)
gen_box.style.update(direction=COLUMN, alignment='center')
self.main_box.style.update(direction=COLUMN,
padding=30,
alignment='center')
self.main_window = toga.MainWindow(title=self.formal_name,
size=(1000, 600))
self.main_window.content = self.main_box
self.main_window.show()
def update_label(self, widget):
self.logger.info("Updating generation label")
self.genmdeinfo_lab.text = self.mode_info[widget.value]
def set_btns(self, value):
if self.profile_manager.cur_prf == "No Profile":
self.gen_btn.enabled = False
self.dir_btn.enabled = False
self.rtf_btn.enabled = False
self.rep_btn.enabled = False
else:
self.gen_btn.enabled = value
self.dir_btn.enabled = value
self.rtf_btn.enabled = value
self.rep_btn.enabled = value
def _set_profile_status(self, e):
self.logger.info("switch profile: {}".format(e.value))
if e.value is None:
self.logger.info("catch none {}".format(
self.profile_manager.cur_prf))
elif e.value == self.profile_manager.cur_prf:
self.logger.info("catch same values")
else:
name = e.value
self.profile_manager.load_profile(name)
self._refresh_inp()
self.set_btns(True)
Config_Manager().save_config(
str(self.paths.app) + "/.user/cfg.json",
self.profile_manager.config)
def _refresh_inp(self, clear=False):
self.logger.info("Refresh Input Buttons")
if clear:
self.dir_inp.clear()
self.rtf_inp.clear()
else:
self.dir_inp.value = self.profile_manager.prf_cfg['img_dir']
self.rtf_inp.value = self.profile_manager.prf_cfg['rtf']
def _create_profile(self, ent, c):
name = ent.value
self.profile_manager.create_profile(name)
ent.clear()
c.add_item(name)
def _delete_profile(self, c):
prf = c.value
self.profile_manager.delete_profile(prf)
c.remove_item(prf)
self._refresh_inp(True)
self.set_btns(False)
def _throw_error(self, msg):
self.logger.info("Error window {}:".format(msg))
self.main_window.error_dialog('Error', msg)
def _show_info(self, msg):
self.logger.info("Info window: {}".format(msg))
self.main_window.info_dialog("Info", msg)
def action_select_folder_dialog(self, widget):
self.logger.info("Select Folder...")
try:
path_names = self.main_window.select_folder_dialog(
title="Select image root folder")
self.dir_inp.value = path_names[0] + "/"
self.profile_manager.prf_cfg['img_dir'] = path_names[0] + "/"
Config_Manager().save_config(
str(self.paths.app) + "/.user/" +
self.profile_manager.cur_prf + ".json",
self.profile_manager.prf_cfg)
except Exception:
pass
def action_open_file_dialog(self, widget):
self.logger.info("Select File...")
try:
fname = self.main_window.open_file_dialog(title="Open RTF file",
multiselect=False,
file_types=['rtf'])
self.logger.info("Created file-dialog")
if fname is not None:
self.rtf_inp.value = fname
self.profile_manager.prf_cfg['rtf'] = fname
Config_Manager().save_config(
str(self.paths.app) + "/.user/" +
self.profile_manager.cur_prf + ".json",
self.profile_manager.prf_cfg)
else:
self.profile_manager.prf_cfg['rtf'] = ""
self.rtf_inp.value = ""
Config_Manager().save_config(
str(self.paths.app) + "/.user/" +
self.profile_manager.cur_prf + ".json",
self.profile_manager.prf_cfg)
except Exception:
self.logger.error("Fatal error in main loop", exc_info=True)
pass
def _replace_faces(self, widget):
self.logger.info("Start Replace Faces")
# get values from UI elements
rtf = self.profile_manager.prf_cfg['rtf']
img_dir = self.profile_manager.prf_cfg['img_dir']
profile = self.profile_manager.cur_prf
mode = self.genmde_lst.value
if not os.path.isfile(rtf):
self._throw_error("The RTF file doesn't exist!")
self.gen_prg.stop()
self.profile_manager.prf_cfg['rtf'] = ''
return
if not os.path.isdir(img_dir):
self._throw_error("The image directory doesn't exist!")
self.gen_prg.stop()
self.profile_manager.prf_cfg['img_dir'] = ''
return
self.logger.info("rtf: {}".format(rtf))
self.logger.info("img_dir: {}".format(img_dir))
self.logger.info("profile: {}".format(profile))
self.logger.info("mode: {}".format(mode))
self.gen_prg.start()
self.gen_prg.update_label("Parsing RTF")
yield 0.1
rtf_data = RTF_Parser().parse_rtf(rtf)
self.gen_prg.update_progress(20)
self.gen_prg.update_label("Map player to ethnicity")
yield 0.1
mapping_data = Mapper(img_dir, self.profile_manager).generate_mapping(
rtf_data, mode)
self.gen_prg.update_progress(60)
self.gen_prg.update_label("Generate config.xml")
yield 0.1
self.profile_manager.write_xml(mapping_data)
# save profile metadata (used pics and config.xml)
self.gen_prg.update_label("Save metadata for profile")
self.gen_prg.update_progress(10)
yield 0.1
Config_Manager().save_config(
str(self.paths.app) + "/.user/" + profile + ".json",
self.profile_manager.prf_cfg)
self.gen_prg.update_progress(10)
yield 0.1
self.gen_prg.update_label("Finished! :)")
yield 0.1
self._show_info("Finished! :)")
self.gen_prg.stop()
def change_image(self, id):
self.logger.info("try to change image preview")
uid = id.value
try:
img_name = self.prf_cfg["imgs"][uid]
img_eth = self.prf_cfg["ethnics"][uid]
img_path = self.prf_cfg["img_dir"] + "/" + img_eth + "/" + img_name
self.rep_img.image = toga.Image(img_path)
self.logger.info("change image preview to: {}".format(img_path))
except Exception:
self.logger.info("changing image preview failed!")
return
def send_report(self, e):
uid = self.rep_inp.value
img_name = self.prf_cfg["imgs"][uid]
img_eth = self.prf_cfg["ethnics"][uid]
img_path = img_eth + "/" + img_name
img_file = self.rep_img.image.path
self.logger.info("send report: {}".format(img_file))
hook = Webhook(
"https://discord.com/api/webhooks/770397581149863946/Wls0g6LEyTXEpOqzfLn2YuDRKANFSAFpwKe62VL9IxpwsQDWFjYHVfy19hrYiv5p0X2a"
)
embed = Embed(
description='A user reported the following face',
color=0x5CDBF0,
timestamp='now' # sets the timestamp to current time
)
file = File(img_file)
embed.add_field(name='File', value=img_path)
hook.send(embed=embed, file=file)
self._show_info("Thanks for Reporting!")
def main(proteome_file, output_dir):
all_proteins = list() # all_proteins[i] = PROTEIN()_OBJECT
protein_seq = dict() # protein_seq[GENE_NAME] = AMINO_ACID_SEQUENCE
print "Reading Uniprot file and generating k-mers list for each protein..."
created_protein_names = set(
) # prevent creation of two similar protein objects
for rec in SeqIO.parse(open(proteome_file), 'fasta'):
seq = str(rec.seq)
uniqueIdentifier, entryName, proteinName, organismName, geneName = \
utils.parse_UniProtKB_header(rec.description)
if geneName == '':
geneName = uniqueIdentifier
#print 'Using uncharacterized gene with identifier %s' % uniqueIdentifier
#print 'Ignoring unknown gene: %s' % rec.description
#continue
if geneName in created_protein_names:
print 'Ignoring duplicate gene: %s' % rec.description
continue
# create a new Protein object
created_protein_names.add(geneName)
protein_seq[geneName] = seq
all_proteins.append(Protein(geneName, seq, params.K))
print
print "Counted k-mer (k=%d) for %d different genes (proteins)." % (
params.K, len(all_proteins))
pb = Progressbar('Generating frequency dictionary for k-mers')
skipped_prots = 0
kmers_frequency = dict() # track popularity of kmer accross all proteins
i = 0
for prot in all_proteins:
i += 1
pb.update_progress(i, len(all_proteins))
"""
if prot.geneName.startswith('ZNF') or prot.geneName.startswith('ZF'):
skipped_prots += 1
continue
if prot.geneName.startswith('OR'):
skipped_prots += 1
continue
if prot.geneName.startswith('HOX'):
skipped_prots += 1
continue
if prot.geneName.startswith('IGKV'):
skipped_prots += 1
continue
"""
for kmer in prot.kmers:
if kmer not in kmers_frequency:
kmers_frequency[kmer] = set()
kmers_frequency[kmer].add(prot.geneName)
print "Sorting frequent k-mers by frequency..."
most_frequenct_kmers = sorted(kmers_frequency,
key=lambda k: len(kmers_frequency[k]),
reverse=True)
import datetime, time, csv
timestamp = datetime.datetime.fromtimestamp(
time.time()).strftime('%Y-%m-%d-%H%M%S')
outfile = '{}/frequent k{}-mers - {}.csv'.format(output_dir, params.K,
timestamp)
with open(outfile, "wb") as csv_file:
writer = csv.writer(csv_file, delimiter=',')
writer.writerow([
'k-mer', 'number of proteins', 'percentage of total', 'all',
'(Out of %d proteins in total)' %
(len(all_proteins) - skipped_prots)
])
for kmer in most_frequenct_kmers:
total_proteins = len(kmers_frequency[kmer])
if total_proteins < 10:
break
percentage = "{0:.4f}".format(
float(total_proteins) / (len(all_proteins) - skipped_prots))
geneList = list(kmers_frequency[kmer])
#geneList = '\r\n'.join(geneList)
row = [kmer, total_proteins, percentage, geneList]
writer.writerow(row)
if geneName == '':
print 'Ignoring unknown gene: %s' % rec.description
continue
if geneName in created_protein_names:
print 'Ignoring duplicate gene: %s' % rec.description
continue
# create a new Protein object
created_protein_names.add(geneName)
protein_seq[geneName] = seq
all_proteins.append(Protein(geneName, seq, params.K))
print
print "Counted k-mer (k=%d) for %d different genes (proteins)." % (
params.K, len(all_proteins))
pb = Progressbar('Generating frequency dictionary for k-mers')
kmers_frequency = dict() # track popularity of kmer accross all proteins
i = 0
for prot in all_proteins:
i += 1
pb.update_progress(i, len(all_proteins))
for kmer in prot.kmers:
if kmer not in kmers_frequency:
kmers_frequency[kmer] = set()
# add the new protein only if it's dissimilar enough from all other
# proteins that were already added and contain this kmer
protein_names = kmers_frequency[
kmer] # list of all prots that share this kmer
redundantProt = False
def run(self):
prg = Progressbar()
prg.run(self._sprun, self.init_delay)
) # prevent creation of two similar protein objects
for rec in SeqIO.parse(open(params.PROTEOME_FILE), 'fasta'):
seq = str(rec.seq)
uniqueIdentifier, entryName, proteinName, organismName, geneName = \
utils.parse_UniProtKB_header(rec.description)
if geneName == '':
print 'Ignoring unknown gene: %s' % rec.description
continue
if geneName in created_protein_names:
print 'Ignoring duplicate gene: %s' % rec.description
continue
# create a new Protein object
created_protein_names.add(geneName)
protein_seq[geneName] = seq
pb = Progressbar('Diluting similar proteins')
diluted_genes_in_connected_component = set()
i = 0
for gene1 in genes_in_connected_component:
i += 1
pb.update_progress(i, len(genes_in_connected_component))
redundantProt = False
for gene2 in diluted_genes_in_connected_component:
if not utils.proteins_are_dissimilar(gene1, gene2, protein_seq[gene1],
protein_seq[gene2]):
redundantProt = True
break
if not redundantProt:
diluted_genes_in_connected_component.add(gene1)
print "Total genes in connected component: %s" % len(