def upload_file():
if request.method == 'POST':
session['db'] = 'hg38' # use the latest genome by default
if 'db' in request.form:
if request.form['db'] == 'hg19':
session['db'] = 'hg19'
elif request.form['db'] != 'hg38':
flash('Unsuported genome option %s. Using hg38.' %
(request.form['session']))
else:
flash('Genome not specified. Using hg38.')
# Set up the Spreadhseet Column for this run
session['chromcol'] = '#CHROM'
session['poscol'] = 'POS'
session['refcol'] = 'REF'
if 'chromcol' in request.form and \
request.form['chromcol'] != session['chromcol']:
session['chromcol'] = request.form['chromcol']
flash("Using %s as chromosome column name" % (session['chromcol']))
if 'poscol' in request.form and \
request.form['poscol'] != session['poscol']:
session['poscol'] = request.form['poscol']
flash("Using %s as position column name" % (session['poscol']))
if 'refcol' in request.form and \
request.form['refcol'] != session['refcol']:
session['refcol'] = request.form['refcol']
flash("Using %s as reference column name" % (session['refcol']))
# Set up the Sequence Options for this run
session['bracketlen'] = 500
session['primerlen'] = '200-500'
if 'bracketlen' in request.form and \
int(request.form['bracketlen']) != session['bracketlen']:
session['bracketlen'] = int(request.form['bracketlen'])
flash("Using %d as bracketed sequence length" %
(session['bracketlen']))
if 'primerlen' in request.form and \
request.form['primerlen'] != session['primerlen']:
session['primerlen'] = request.form['primerlen']
flash("Using %s as Primer3 sequence length range" %
(session['primerlen']))
file = request.files['file']
if file and allowed_file(file.filename):
filename = secure_filename(file.filename)
path = os.path.join(app.config['UPLOAD_FOLDER'], filename)
file.save(path)
createSession()
session['filename'] = filename
if filename[-3:] == 'csv':
rows = fileutils.readCsv(path)
else:
rows = fileutils.readExcel(path)
session['totalRows'] = len(rows)
genomePath = "genomes"
if session['db'] == 'hg19':
genomeFile = "hg19.2bit"
else:
session['db'] = 'hg38'
genomeFile = "hg38.2bit"
genomeFilePath = "/".join([genomePath, genomeFile])
pr_args = [
rows,
genomeFilePath,
session['db'],
session['chromcol'],
session['poscol'],
session['refcol'],
session['bracketlen'],
session['primerlen'],
]
task = processRows.apply_async(args=pr_args)
logger.info('Created task with id %s' % (task.id))
return render_template('status.html',
myfunc='primers',
task_id=task.id)
else:
if not file:
flash("You must specify a file.")
else:
flash("Invalid filename. File extensions may include: %s." %
(", ".join(ALLOWED_EXTENSIONS)))
# if not post, return index.html
return render_template('index.html')
def upload_file():
if request.method == 'POST':
session['db'] = 'hg38' # use the latest genome by default
if 'db' in request.form:
if request.form['db'] == 'hg19':
session['db'] = 'hg19'
elif request.form['db'] != 'hg38':
flash('Unsuported genome option %s. Using hg38.'
%(request.form['session']))
else:
flash('Genome not specified. Using hg38.')
# Set up the Spreadhseet Column for this run
session['chromcol'] = '#CHROM'
session['poscol'] = 'POS'
session['refcol'] = 'REF'
if 'chromcol' in request.form and \
request.form['chromcol'] != session['chromcol']:
session['chromcol'] = request.form['chromcol']
flash("Using %s as chromosome column name"%(session['chromcol']))
if 'poscol' in request.form and \
request.form['poscol'] != session['poscol']:
session['poscol'] = request.form['poscol']
flash("Using %s as position column name"%(session['poscol']))
if 'refcol' in request.form and \
request.form['refcol'] != session['refcol']:
session['refcol'] = request.form['refcol']
flash("Using %s as reference column name"%(session['refcol']))
# Set up the Sequence Options for this run
session['bracketlen'] = 500
session['primerlen'] = '200-500'
if 'bracketlen' in request.form and \
int(request.form['bracketlen']) != session['bracketlen']:
session['bracketlen'] = int(request.form['bracketlen'])
flash("Using %d as bracketed sequence length"%(session['bracketlen']))
if 'primerlen' in request.form and \
request.form['primerlen'] != session['primerlen']:
session['primerlen'] = request.form['primerlen']
flash("Using %s as Primer3 sequence length range"%(session['primerlen']))
file = request.files['file']
if file and allowed_file(file.filename):
filename = secure_filename(file.filename)
path = os.path.join(app.config['UPLOAD_FOLDER'],filename)
file.save(path)
createSession()
session['filename'] = filename
if filename[-3:] == 'csv':
rows = fileutils.readCsv(path)
else:
rows = fileutils.readExcel(path)
session['totalRows'] = len(rows)
genomePath = "genomes"
if session['db'] == 'hg19':
genomeFile = "hg19.2bit"
else:
session['db'] = 'hg38'
genomeFile = "hg38.2bit"
genomeFilePath = "/".join([genomePath,genomeFile])
pr_args = [rows,
genomeFilePath,
session['db'],
session['chromcol'],
session['poscol'],
session['refcol'],
session['bracketlen'],
session['primerlen'],
]
task = processRows.apply_async(args=pr_args)
logger.info('Created task with id %s'%(task.id))
return render_template('status.html', myfunc='primers', task_id=task.id)
else:
if not file:
flash("You must specify a file.")
else:
flash("Invalid filename. File extensions may include: %s."%
(", ".join(ALLOWED_EXTENSIONS)))
# if not post, return index.html
return render_template('index.html')
def multiple_sites():
if request.method == 'POST':
session['db'] = 'hg38' # use the latest genome by default
if 'db' in request.form:
if request.form['db'] == 'hg19':
session['db'] = 'hg19'
elif request.form['db'] != 'hg38':
flash('Unsuported genome option %s. Using hg38.' %
(request.form['session']))
else:
flash('Genome not specified. Using hg38.')
session['chromcol'] = '#CHROM'
session['poscol'] = 'POS'
session['varcol'] = 'VARIANT'
if 'chromcol' in request.form and \
request.form['chromcol'] != session['chromcol']:
session['chromcol'] = request.form['chromcol']
flash("Using %s as chromosome column name" % (session['chromcol']))
if 'poscol' in request.form and \
request.form['poscol'] != session['poscol']:
session['poscol'] = request.form['poscol']
flash("Using %s as position column name" % (session['poscol']))
if 'varcol' in request.form and \
request.form['varcol'] != session['varcol']:
session['varcol'] = request.form['varcol']
flash("Using %s as variant column name" % (session['varcol']))
file = request.files['file']
if file and allowed_file(file.filename):
filename = secure_filename(file.filename)
path = os.path.join(app.config['UPLOAD_FOLDER'], filename)
file.save(path)
createSession()
session['filename'] = filename
if filename[-3:] == 'csv':
rows = fileutils.readCsv(path)
else:
rows = fileutils.readExcel(path)
session['totalRows'] = len(rows)
genomePath = "genomes"
if session['db'] == 'hg19':
genomeFile = "hg19.2bit"
else:
session['db'] = 'hg38'
genomeFile = "hg38.2bit"
genomeFilePath = "/".join([genomePath, genomeFile])
#predictSpliceSites(session['uuid'],
# rows,
# genomeFilePath,
# db=session['db'],
# chromcol=session['chromcol'],
# poscol=session['poscol'],
# varcol=session['varcol'],
# )
#return render_template('predictionstatus.html')
pr_args = [
rows,
genomeFilePath,
session['db'],
session['chromcol'],
session['poscol'],
session['varcol'],
]
task = predictSpliceSites.apply_async(args=pr_args)
logger.info('Created task with id %s' % (task.id))
return render_template('status.html',
myfunc='predictions',
task_id=task.id)
return render_template('index.html')
def multiple_sites():
if request.method == 'POST':
session['db'] = 'hg38' # use the latest genome by default
if 'db' in request.form:
if request.form['db'] == 'hg19':
session['db'] = 'hg19'
elif request.form['db'] != 'hg38':
flash('Unsuported genome option %s. Using hg38.'
%(request.form['session']))
else:
flash('Genome not specified. Using hg38.')
session['chromcol'] = '#CHROM'
session['poscol'] = 'POS'
session['varcol'] = 'VARIANT'
if 'chromcol' in request.form and \
request.form['chromcol'] != session['chromcol']:
session['chromcol'] = request.form['chromcol']
flash("Using %s as chromosome column name"%(session['chromcol']))
if 'poscol' in request.form and \
request.form['poscol'] != session['poscol']:
session['poscol'] = request.form['poscol']
flash("Using %s as position column name"%(session['poscol']))
if 'varcol' in request.form and \
request.form['varcol'] != session['varcol']:
session['varcol'] = request.form['varcol']
flash("Using %s as variant column name"%(session['varcol']))
file = request.files['file']
if file and allowed_file(file.filename):
filename = secure_filename(file.filename)
path = os.path.join(app.config['UPLOAD_FOLDER'],filename)
file.save(path)
createSession()
session['filename'] = filename
if filename[-3:] == 'csv':
rows = fileutils.readCsv(path)
else:
rows = fileutils.readExcel(path)
session['totalRows'] = len(rows)
genomePath = "genomes"
if session['db'] == 'hg19':
genomeFile = "hg19.2bit"
else:
session['db'] = 'hg38'
genomeFile = "hg38.2bit"
genomeFilePath = "/".join([genomePath,genomeFile])
#predictSpliceSites(session['uuid'],
# rows,
# genomeFilePath,
# db=session['db'],
# chromcol=session['chromcol'],
# poscol=session['poscol'],
# varcol=session['varcol'],
# )
#return render_template('predictionstatus.html')
pr_args = [rows,
genomeFilePath,
session['db'],
session['chromcol'],
session['poscol'],
session['varcol'],
]
task = predictSpliceSites.apply_async(args=pr_args)
logger.info('Created task with id %s'%(task.id))
return render_template('status.html', myfunc='predictions', task_id=task.id)
return render_template('index.html')