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GUI.py
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GUI.py
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# -*- coding: utf-8 -*-
# @Time : 2020/10/04 21:00
# @Author : Zhongyi Hua
# @FileName: GUI.py
# @Usage: The GUI interface for IdenDSS
# @Note:
# @E-mail: njbxhzy@hotmail.com
from pathlib import Path
import logging
import PySimpleGUI as sg
from IdenDSS.identification import iden_main
from IdenDSS.plugins import IndexDb, search_rflp, combine_dss, summary_dss, flanking, convert
from IdenDSS.validation import v_main
from IdenDSS.utils import enzymes_list, SettingInfo, DataInfo
def index_tab():
"""
The tab for indexing database
"""
row1 = sg.Frame('Data setting', [
[sg.T('Input path:', size=15), sg.I(key='-INDEX INPUT-', size=45), sg.FileBrowse(target='-INDEX INPUT-')],
[sg.T('Output path:', size=15), sg.I(key='-INDEX OUTPUT-', size=45), sg.FolderBrowse(target='-INDEX OUTPUT-')],
[sg.T('DSS length:', size=15), sg.I('40', key='-INDEX LENGTH-', size=5)]
])
row2 = sg.Frame('Global setting', [
[sg.T('Bin directory path (Optional):', size=30), sg.I(key='-INDEX BIN_DIR-'), sg.FolderBrowse(target='-INDEX BIN_DIR-')]
])
main_col = [
[row1],
[row2]
]
return sg.Tab('index', layout=main_col, expand_x = True)
def iden_tab():
"""
The tab for identifying DSS
"""
row1 = sg.Frame('Data setting', [
[sg.T('Input path:', size=15), sg.I(key='-IDEN INPUT-', size=45), sg.FileBrowse(target='-IDEN INPUT-')],
[sg.T('Output path:', size=15), sg.I(key='-IDEN OUTPUT-', size=45), sg.FolderBrowse(target='-IDEN OUTPUT-')],
[sg.T('Database path:', size=15), sg.I(key='-IDEN DATABASE-', size=45), sg.FileBrowse(target='-IDEN DATABASE-')],
[sg.T('DSS length:', size=15), sg.I('40', key='-IDEN LENGTH-', size=5)]
])
row2 = sg.Frame('Global setting', [
[sg.T('Temporary directory path (Optional):', size=30), sg.I(key='-IDEN TMP_DIR-'), sg.FolderBrowse(target='-IDEN TMP_DIR-')],
[sg.T('Bin directory path (Optional):', size=30), sg.I(key='-IDEN BIN_DIR-'), sg.FolderBrowse(target='-IDEN BIN_DIR-')],
[sg.T('Threads (Optional):', size=30), sg.I('4', key='-IDEN THREADS-')]
])
main_col = [
[row1],
[row2]
]
return sg.Tab('identify', layout=main_col, expand_x = True)
def plugin_tab():
"""
The tab for plugin
"""
row1 = sg.Frame('Option', [
[sg.Checkbox('Combine', k='-COMBINE-'),
sg.Checkbox('RFLP', k='-RFLP-'),
sg.Checkbox('Statistic', k='-STATISTIC-'),
sg.Checkbox('Convert', k='-CONVERT-')],
[sg.Checkbox('Flanking', k='-FLANK-'), sg.I('200', key='-FLANK VALUE-')],
[sg.Checkbox('Sample', k='-SAMPLE-'), sg.I('5', key='-SAMPLE VALUE-')]
])
row2 = sg.Frame('Data setting', [
[sg.T('Input path:', size=15), sg.I(key='-PLUG INPUT-', size=45), sg.FileBrowse(target='-PLUG INPUT-')],
[sg.T('Output path:', size=15), sg.I(key='-PLUG OUTPUT-', size=45), sg.FolderBrowse(target='-PLUG OUTPUT-')],
[sg.T('Database path:', size=15), sg.I(key='-PLUG DATABASE-', size=45), sg.FileBrowse(target='-PLUG DATABASE-')]
])
row3 = sg.Frame('Global setting', [
[sg.T('Temporary directory path (Optional):', size=30), sg.I(key='-PLUG TMP_DIR-'), sg.FolderBrowse(target='-PLUG TMP_DIR-')]
])
main_col = [
[row1],
[row2],
[row3]
]
return sg.Tab('plugin', layout=main_col, expand_x = True)
def validate_tab():
"""
The tab for validation
"""
row1 = sg.Frame('Data setting', [
[sg.T('Input path:', size=18),
sg.I(key='-VALI INPUT-', size=42),
sg.FileBrowse(target='-VALI INPUT-')],
[sg.T('Species fastq path:', size=18),
sg.ML(key='-VALI SP-', size=(40,2)),
sg.I(visible=False, key='-VALI SP MULTIIN-', enable_events=True),
sg.FilesBrowse(target='-VALI SP MULTIIN-', file_types=(('fastq', '.fastq .fq'),))],
[sg.T('Background fastq path:', size=18),
sg.ML(key='-VALI BG-', size=(40,2)),
sg.I(visible=False, key='-VALI BG MULTIIN-', enable_events=True),
sg.FilesBrowse(target='-VALI BG MULTIIN-', file_types=(('fastq', '.fastq .fq'),))],
[sg.T('Output path:', size=18),
sg.I(key='-VALI OUTPUT-', size=42),
sg.FolderBrowse(target='-VALI OUTPUT-')]
])
row2 = sg.Frame('Global setting', [
[sg.T('Temporary directory path (Optional):', size=30), sg.I(key='-VALI TMP_DIR-'), sg.FolderBrowse(target='-VALI TMP_DIR-')],
[sg.T('Bin directory path (Optional):', size=30), sg.I(key='-VALI BIN_DIR-'), sg.FolderBrowse(target='-VALI BIN_DIR-')]
])
main_col = [
[row1],
[row2]
]
return sg.Tab('validate', layout=main_col, expand_x = True)
def make_window():
"""
Make the main window
"""
sg.theme('SystemDefaultForReal')
tab1 = index_tab()
tab2 = iden_tab()
tab3 = plugin_tab()
tab4 = validate_tab()
layout = [
[sg.TabGroup([[tab1, tab2, tab3, tab4]], key='-TASK-')],
[sg.CB('This is a circular DNA sequence Database', k='-CIRCULAR-')],
[sg.ML('',
size=(60,5),
k='-OUT-',
write_only=True,
expand_x=True,
reroute_stdout=True,
reroute_stderr=True,
echo_stdout_stderr=True,
reroute_cprint=True,
auto_refresh=True,
autoscroll=True)],
[sg.Button('Run', key='run'), sg.Exit()]
]
window = sg.Window('IdenDSS', layout, default_element_size=(30,1))
return window
def main():
"""
The main interface for event loop
"""
window = make_window()
logger = logging.getLogger('IdenDSS')
logger.setLevel(level=logging.INFO)
# Setting a special Handler for Logger to work with PySimpleGUI is necessary
view_handler = logging.StreamHandler()
logger.addHandler(view_handler)
while True:
event, values = window.read()
if event in (sg.WINDOW_CLOSED, 'Exit'):
break
if event.endswith('MULTIIN-'):
# for multiline box input. use "-* MULTIIN-" for invisible input box.
multi_key = ' '.join(event.split(' ')[:-1]) + '-'
window[multi_key].Update('\n'.join(values[event].split(';')) + '\n', append=True)
if event == 'run':
if values['-TASK-'] == 'index':
set_info = SettingInfo(
bin_dir=Path(values['-INDEX BIN_DIR-']),
logger=logger)
data_info = DataInfo(
in_put=Path(values['-INDEX INPUT-']),
output=Path(values['-INDEX OUTPUT-']),
circular=values['-CIRCULAR-'],
length=int(values['-INDEX LENGTH-'])
)
index_db = IndexDb(data_info, set_info)
index_db.index()
elif values['-TASK-'] == 'identify':
set_info = SettingInfo(
tmp=Path(values['-IDEN TMP_DIR-']),
bin_dir=Path(values['-IDEN BIN_DIR-']),
threads=Path(values['-IDEN THREADS-'],
logger=logger)
)
data_info = DataInfo(
in_put=Path(values['-IDEN INPUT-']),
output=Path(values['-IDEN OUTPUT-']),
db=Path(values['-IDEN DATABASE-']),
length=int(values['-IDEN LENGTH-']),
circular=values['-CIRCULAR-']
)
iden_main(data_info, set_info)
elif values['-TASK-'] == 'plugin':
set_info = SettingInfo(
tmp=Path(values['-PLUG TMP_DIR-']),
logger=logger)
set_info.clean_file(Path(values['-PLUG INPUT-']))
data_info = DataInfo(
in_put=Path(values['-PLUG INPUT-']),
output=Path(values['-PLUG OUTPUT-']),
db=Path(values['-PLUG DATABASE-']),
circular=values['-CIRCULAR-'])
if values['-RFLP-']:
search_rflp(data_info, set_info, enzymes_list)
if values['-COMBINE-']:
combine_dss(data_info, set_info)
if values['-STATISTIC-']:
summary_dss(data_info, set_info)
if values['-FLANK-']:
data_info.length = int(values['-FLANK VALUE'])
flanking(data_info, set_info)
if values['-CONVERT-']:
convert(data_info, set_info)
if values['-SAMPLE-']:
data_info.length = int(values['-SAMPLE VALUE'])
convert(data_info, set_info)
elif values['-TASK-'] == 'validate':
set_info = SettingInfo(
tmp=Path(values['-VALI TMP_DIR-']),
bin_dir=Path(values['-VALI BIN_DIR-']),
logger=logger)
data_info = DataInfo(in_put=Path(values['-VALI INPUT-']),
output=Path(values['-VALI OUTPUT-']),
db=[Path(_) for _ in values['-VALI BG-'].split('\n')],
db2=[Path(_) for _ in values['-VALI SP-'].split('\n')])
v_main(data_info, set_info)
window.close()
if __name__ == '__main__':
main()