def custom_db_analysis():
# Deal with a custom database file
import os
import glob
import shutil
from genewordsearch.DBBuilder import geneWordBuilder
# Prep the database files for processing
ip = str(request.environ['REMOTE_ADDR'])
folder = os.path.join(app.config['UPLOAD_FOLDER'], ip)
os.makedirs(folder, exist_ok=True)
dbFiles = request.files.getlist('geneDBs')
fileCount = len(dbFiles)
fileNum = 0
for db in dbFiles:
filename = secure_filename(db.filename)
db.save(os.path.join(folder, (str(fileNum)+filename[-4:])))
fileNum += 1
fileList = glob.glob(folder+'/*')
fileList.sort()
# Pull and organize the rest of the database info
headers = []
headtxt = []
delimiters = []
geneCols = []
desCols = []
fileNum = 0
while(fileNum < fileCount):
headtxt.append(str(request.form['header'+str(fileNum)]))
delimiters.append(str(request.form['delimiter'+str(fileNum)]))
geneCols.append(str(request.form['geneCol'+str(fileNum)]))
desCols.append(str(request.form['desCols'+str(fileNum)]))
fileNum += 1
for header in headtxt:
if(header =='y'):
headers.append(True)
else:
headers.append(False)
geneWordBuilder(ip,fileList,geneCols,desCols,delimiters,headers)
shutil.rmtree(folder+'/')
# Run the enrichment analysis
genes = str(request.form['geneList'])
probCutoff = float(request.form['probCut'])
genes = re.split('\r| |,|\t|\n',genes)
genes = list(filter((lambda x: x != ''),genes))
try:
results = geneWordSearch(genes,ip,minChance=probCutoff)
except KeyError:
abort(400)
ans = WordFreq.to_JSON_array(results[0])
shutil.rmtree('genewordsearch/databases/'+ip+'/')
return jsonify(result=ans)
def custom_db_analysis():
# Deal with a custom database file
# Prep the database files for processing
ip = str(request.environ['REMOTE_ADDR'])
folder = os.path.join(app.config['UPLOAD_FOLDER'], ip)
os.makedirs(folder, exist_ok=True)
dbFiles = request.files.getlist('geneDBs')
fileCount = len(dbFiles)
fileNum = 0
for db in dbFiles:
filename = secure_filename(db.filename)
db.save(os.path.join(folder, (str(fileNum) + filename[-4:])))
fileNum += 1
fileList = glob.glob(folder + '/*')
fileList.sort()
# Pull and organize the rest of the database info
headers = []
headtxt = []
delimiters = []
geneCols = []
desCols = []
fileNum = 0
while (fileNum < fileCount):
headtxt.append(str(request.form['header' + str(fileNum)]))
delimiters.append(str(request.form['delimiter' + str(fileNum)]))
geneCols.append(str(request.form['geneCol' + str(fileNum)]))
desCols.append(str(request.form['desCols' + str(fileNum)]))
fileNum += 1
for header in headtxt:
if (header == 'y'):
headers.append(True)
else:
headers.append(False)
geneWordBuilder(ip, fileList, geneCols, desCols, delimiters, headers)
shutil.rmtree(folder + '/')
# Run the enrichment analysis
genes = str(request.form['geneList'])
probCutoff = float(request.form['probCut'])
genes = re.split('\r| |,|\t|\n', genes)
genes = list(filter((lambda x: x != ''), genes))
try:
results = geneWordSearch(genes, ip, minChance=probCutoff)
except KeyError:
abort(400)
ans = WordFreq.to_JSON_array(results[0])
shutil.rmtree('genewordsearch/databases/' + ip + '/')
return jsonify(result=ans)
def gene_word_search():
cob = networks[str(request.form['network'])]
pCutoff = safeOpts('pCutoff',float(request.form['pCutoff']))
geneList = str(request.form['geneList'])
geneList = list(filter((lambda x: x != ''), re.split('\r| |,|;|\t|\n', geneList)))
# Run the analysis and return the JSONified results
if cob._global('parent_refgen') in func_data_db:
results = geneWordSearch(geneList, cob._global('parent_refgen'), minChance=pCutoff)
else:
abort(405)
if len(results[0]) == 0:
abort(400)
results = WordFreq.to_JSON_array(results[0])
return jsonify(result=results)
def gene_word_search():
cob = networks[str(request.form['network'])]
pCutoff = safeOpts('pCutoff',float(request.form['pCutoff']))
geneList = str(request.form['geneList'])
geneList = list(filter((lambda x: x != ''), re.split('\r| |,|;|\t|\n', geneList)))
# Run the analysis and return the JSONified results
if hasGWS and (cob._global('parent_refgen') in func_data_db):
results = geneWordSearch(geneList, cob._global('parent_refgen'), minChance=pCutoff)
else:
abort(405)
if len(results[0]) == 0:
abort(400)
results = WordFreq.to_JSON_array(results[0])
return jsonify(result=results)
def gene_analysis():
# Run the genes through genewordsearch
# Sanitize the input
species = str(request.form['species'])
genes = str(request.form['geneList'])
probCutoff = float(request.form['probCut'])
genes = re.split('\r| |,|\t|\n', genes)
genes = list(filter((lambda x: x != ''), genes))
# Run the analysis and return the JSONified results
try:
results = geneWordSearch(genes, species, minChance=probCutoff)
except KeyError:
abort(400)
ans = WordFreq.to_JSON_array(results[0])
return jsonify(result=ans)
def gene_analysis():
# Run the genes through genewordsearch
# Sanitize the input
species = str(request.form['species'])
genes = str(request.form['geneList'])
probCutoff = float(request.form['probCut'])
genes = re.split('\r| |,|\t|\n',genes)
genes = list(filter((lambda x: x != ''),genes))
# Run the analysis and return the JSONified results
try:
results = geneWordSearch(genes,species,minChance=probCutoff)
except KeyError:
abort(400)
ans = WordFreq.to_JSON_array(results[0])
return jsonify(result=ans)