def update_protein_options(upload_contents, preloaded):
dropdown_options = [
{'label': 1, 'value': 0}
]
if preloaded is not None:
proteins = pr.read_fasta(preloaded)
elif upload_contents is not None and preloaded is None:
data = ''
try:
content_type, content_string = upload_contents.split(',')
data = base64.b64decode(content_string).decode('UTF-8')
except AttributeError:
pass
proteins = pr.read_fasta(data, is_datafile=False)
else:
return dropdown_options
if isinstance(proteins, list):
dropdown_options = []
for i in range(len(proteins)):
dropdown_options.append(dict(
label=i+1,
value=i
))
return dropdown_options
def update_sequence_title(_, entry, preloaded, upload_contents):
if entry is None:
return ''
if preloaded is not None:
protein = pr.read_fasta(preloaded)[entry]
elif upload_contents is not None and preloaded is None:
data = ''
try:
content_type, content_string = upload_contents.split(',')
data = base64.b64decode(content_string).decode('UTF-8')
except AttributeError:
pass
if data == '':
return ''
protein = pr.read_fasta(data, is_datafile=False)[entry]
else:
return ''
titles = ['name', 'entry name', 'protein name', 'identifier', 'desc-0']
for t in titles:
try:
return protein['description'][t]
except KeyError:
continue
return ''
def update_desc_info(upload_contents, entry, preloaded):
if entry is None:
return 'Please select an entry.'
if preloaded is not None:
protein = pr.read_fasta(preloaded)[entry]
elif upload_contents is not None and preloaded is None:
data = ''
try:
content_type, content_string = upload_contents.split(',')
data = base64.b64decode(content_string).decode('UTF-8')
except AttributeError:
pass
if data == '':
return []
try:
protein = pr.read_fasta(data, is_datafile=False)[entry]
except Exception:
return ['NA']
else:
return 'Please either upload a file or select one from \
the dropdown.'
desc = []
for key in protein['description']:
tmp = key.title() + ': ' if 'desc-' not in key else '-'
tmp += protein['description'][key]
desc.append(tmp)
desc.append(html.Br())
return desc
def update_sequence(upload_contents, entry, preloaded):
if entry is None:
return ''
if preloaded is not None:
protein = pr.read_fasta(preloaded)[entry]
elif upload_contents is not None and preloaded is None:
data = ''
try:
content_type, content_string = upload_contents.split(',')
data = base64.b64decode(content_string).decode('UTF-8')
except AttributeError:
pass
if data == '':
return '-'
protein = pr.read_fasta(data, is_datafile=False)[entry]
else:
return '-'
return protein['sequence']
import dash_bio as dashbio
from dash_bio_utils import protein_reader
import dash_html_components as html
external_stylesheets = ['https://codepen.io/chriddyp/pen/bWLwgP.css']
app = dash.Dash(__name__, external_stylesheets=external_stylesheets)
fasta_str = urlreq.urlopen(
'https://raw.githubusercontent.com/plotly/dash-bio-docs-files/master/' +
'sequence_viewer_P01308.fasta').read()
if PY3:
fasta_str = fasta_str.decode('utf-8')
seq = protein_reader.read_fasta(fasta_str, is_datafile=False)[0]['sequence']
app.layout = html.Div([
dashbio.SequenceViewer(id='my-sequence-viewer', sequence=seq),
html.Div(id='sequence-viewer-output')
])
@app.callback(
dash.dependencies.Output('sequence-viewer-output', 'children'),
[dash.dependencies.Input('my-sequence-viewer', 'mouseSelection')])
def update_output(value):
if value is None or len(value) == 0:
return 'There is no mouse selection.'
return 'The mouse selection is {}.'.format(value['selection'])
from dash_bio_utils import protein_reader
import dash_html_components as html
external_stylesheets = ['https://codepen.io/chriddyp/pen/bWLwgP.css']
app = dash.Dash(__name__, external_stylesheets=external_stylesheets)
fasta_str = urlreq.urlopen(
'https://raw.githubusercontent.com/plotly/dash-bio-docs-files/master/' +
'sequence_viewer_P01308.fasta'
).read()
if PY3:
fasta_str = fasta_str.decode('utf-8')
seq = protein_reader.read_fasta(data_string=fasta_str)[0]['sequence']
app.layout = html.Div([
dashbio.SequenceViewer(
id='my-sequence-viewer',
sequence=seq
),
html.Div(id='sequence-viewer-output')
])
@app.callback(
dash.dependencies.Output('sequence-viewer-output', 'children'),
[dash.dependencies.Input('my-sequence-viewer', 'mouseSelection')]
)
def update_output(value):
import json
from dash_bio_utils import pdb_parser, protein_reader, \
styles_parser, xyz_reader
with open('mol3d_model_data.json', 'w+') as f:
f.write(
pdb_parser.create_data(
'../dashbio_demos/dash-molecule-3d-viewer/data/1bna.pdb'))
with open('mol3d_styles_data.json', 'w+') as f:
f.write(
styles_parser.create_style(
'../dashbio_demos/dash-molecule-3d-viewer/data/1bna.pdb',
'cartoon', 'atom'))
with open('sequence_viewer_data.json', 'w+') as f:
f.write(
json.dumps(
protein_reader.read_fasta(
datapath_or_datastring=
'../dashbio_demos/dash-sequence-viewer/data/P01308.fasta.txt')
[0]))
with open('speck_data.json', 'w+') as f:
f.write(
json.dumps(
xyz_reader.read_xyz(
datapath_or_datastring=
'../dashbio_demos/dash-speck/data/methane.xyz')))
import dash_bio as dashbio
from dash_bio_utils import protein_reader
import dash_html_components as html
external_stylesheets = ['https://codepen.io/chriddyp/pen/bWLwgP.css']
app = dash.Dash(__name__, external_stylesheets=external_stylesheets)
fasta_str = urlreq.urlopen(
'https://raw.githubusercontent.com/plotly/dash-bio-docs-files/master/' +
'sequence_viewer_P01308.fasta').read()
if PY3:
fasta_str = fasta_str.decode('utf-8')
seq = protein_reader.read_fasta(datapath_or_datastring=fasta_str,
is_datafile=False)[0]['sequence']
app.layout = html.Div([
dashbio.SequenceViewer(id='my-sequence-viewer', sequence=seq),
html.Div(id='sequence-viewer-output')
])
@app.callback(
dash.dependencies.Output('sequence-viewer-output', 'children'),
[dash.dependencies.Input('my-sequence-viewer', 'mouseSelection')])
def update_output(value):
if value is None or len(value) == 0:
return 'There is no mouse selection.'
return 'The mouse selection is {}.'.format(value['selection'])
import json
from dash_bio_utils import pdb_parser, protein_reader, \
styles_parser, xyz_reader
with open('mol3d_model_data.json', 'w+') as f:
f.write(pdb_parser.create_data(
'../dashbio_demos/sample_data/molecule3d_1bna.pdb'
))
with open('mol3d_styles_data.json', 'w+') as f:
f.write(styles_parser.create_style(
'../dashbio_demos/sample_data/molecule3d_1bna.pdb',
'cartoon',
'atom'
))
with open('sequence_viewer_data.json', 'w+') as f:
f.write(json.dumps(protein_reader.read_fasta(
datapath_or_datastring='../dashbio_demos/sample_data/sequence_viewer_P01308.fasta.txt'
)[0]))
with open('speck_data.json', 'w+') as f:
f.write(json.dumps(xyz_reader.read_xyz(
datapath_or_datastring='../dashbio_demos/sample_data/speck_methane.xyz'
)))
