def process_files(*args):
conn = tinys3.Connection(os.environ.get('AWS_ACCESS_KEY'), os.environ.get('AWS_SECRET_ACCESS_KEY'),
default_bucket=os.environ.get('S3_BUCKET_NAME'))
filename = args[0]
url = "http://s3.amazonaws.com/{}/{}".format(os.environ.get('S3_BUCKET_NAME'), filename)
urllib.urlretrieve(url, filename)
raw_name = os.path.splitext(filename)[0]
Reconcile(args)
freqSummation(args)
with open("{}freqFile.txt".format(raw_name)) as f:
lines = f.readlines()
score_list = ast.literal_eval(lines[0])
total_freq = float(lines[1][:-2])
total_recon = float(lines[3])
total_cost = float(lines[2][:-2])
scoring = args[4]
if scoring == "Frequency":
score_method = "Frequency"
elif scoring == "xscape":
score_method = "Xscape Scoring"
else:
score_method = "Unit Scoring"
results_list = []
for x, score in enumerate(score_list):
tree = treelib1.read_tree("{}.tree".format(raw_name))
stree = treelib1.read_tree("{}{}.stree".format(raw_name, x))
brecon = phylo.read_brecon("{}{}.mowgli.brecon".format(raw_name, x), tree, stree)
output = "{}{}.svg".format(raw_name, x)
phylo.add_implied_spec_nodes_brecon(tree, brecon)
transsvg.draw_tree(tree, brecon, stree, filename=output)
conn.upload(output, open(output, 'rb'), content_type='image/svg+xml')
percent = 100.0 * score / total_freq
running_tot_score = sum(score_list[:x])
running_tot = min(100.0 * running_tot_score / total_freq, 100)
results_list.append((score, percent, running_tot))
return {'results_list': results_list, 'raw_name': raw_name, 'dup': args[1], 'trans': args[2], 'loss': args[3],
'total_cost': total_cost, 'score_method': score_method, 'total_freq': total_freq,
'total_recon': total_recon}
def reconcile(carousel = None):
""" Creates the results page using Master/Reconciliation and vistrans"""
if request.method == 'POST':
file = request.files['newick']
if file:
filename = secure_filename(file.filename)
Name = filename[:-7]
os.system("mkdir "+Name)
f = open(filename, 'w+')
f.write(file.read())
f.close()
os.system("mv "+filename+" "+ Name)
else: return render_template("documentation.html")
if request.form['dup'] != '':
Dup = request.form['dup']
else: Dup = 2
if request.form['trans'] != '':
Trans = request.form['trans']
else: Trans = 3
if request.form['loss'] != '':
Loss = request.form["loss"]
else: Loss = 1
if request.form['switchhigh'] != '':
switchHi = request.form['switchhigh']
else: switchHi = 4.5
if request.form['switchlow'] != '':
switchLo = request.form['switchlow']
else: switchLo = 1.5
if request.form['losshigh'] != '':
lossHi = request.form['losshigh']
else: lossHi = 3
if request.form['losslow'] != '':
lossLo = request.form['losslow']
else: lossLo = 1
path2files = Name + '/' + Name
# os.system("python test.py")
MasterReconciliation.Reconcile(['nothing', path2files+".newick", Dup,
Trans, Loss, request.form["scoring"], switchLo, switchHi, lossLo, lossHi])
reconConversion.freqSummation(["nothing",path2files+".newick",Dup,
Trans, Loss,
request.form["scoring"], switchLo, switchHi, lossLo, lossHi])
with open(path2files + "freqFile.txt") as f:
lines = f.readlines()
scoreList = string2List(lines[0])
totalFreq = float(lines[1][:-2])
totalRecon = float(lines[3])
totalCost = float(lines[2][:-2])
if request.form['scoring'] == "Frequency":
scoreMethod = "Frequency"
elif request.form['scoring'] == "xscape":
scoreMethod = "Xscape Scoring"
else: scoreMethod = "Unit Scoring"
carouselstr = ""
carouselcap= ""
staticString = "<h4>Duplication Cost:" + str(Dup) + ", Transfer Cost: " + \
str(Trans) + ", Loss Cost: " + str(Loss) + "<br>Maximum Parsimony Cost: " + \
str(totalCost) + "<br>Your scoring method: " + scoreMethod + ", Total Sum" + \
" of Scores: " + str(totalFreq) + "<br>Total Number of Optimal " + \
"Reconciliations: " + str(totalRecon) + "</h4>"
for x in range(len(scoreList)):
os.system("python vistrans.py -t " + path2files + ".tree -s " + path2files + \
str(x) + ".stree -b " + path2files + str(x) + ".mowgli.brecon -o " + \
path2files + str(x) + ".svg")
score = scoreList[x]
percent = 100.0*score/totalFreq
if x ==0:
runningTot = percent
carouselstr +='<li data-target="#results" data-slide-to="0" ' + \
'class="active"></li>' + "\n"
carouselcap +="<div class='item active'><img src='/uploads/" + Name + \
str(x) + ".svg' alt='First slide' width='460' height='345'>" + \
"<div class='carousel-caption'><font color='black'><h3>" + \
"Reconciliation 1 of " + str(len(scoreList)) + "</h3><p>Score = " + \
str(score) + "<br>Percent of total = " + str(percent) + "%<br>Running" + \
" total = " + str(runningTot) + "%</font></p></div></div>" + "\n"
os.system("cp /Users/Annalise/GitHub/CompBioSummer2015/" + \
str(path2files) + str(x) + '.svg ' + UPLOAD_FOLDER)
else:
runningTotScore = runningTotal(scoreList, x)
runningTot = 100.0*runningTotScore/totalFreq
if runningTot > 100:
runningTot = 100
carouselstr +='<li data-target="#results" data-slide-to="' + str(x) + \
'"></li>' + "\n"
carouselcap +="<div class='item'><img src='/uploads/" + Name + str(x) + \
".svg' alt='First slide' width='460' height='345'>" + \
"<div class='carousel-caption'><font color='black'><h3>" + \
"Reconciliation " + str(x + 1) + " of " + str(len(scoreList)) + \
"</h3><p>Score = " + str(score) + " <br>Percent of total = " + \
str(percent) + "%<br>Running total = " + str(runningTot) + \
"%</font></p></div></div>" + "\n"
os.system("cp " + path2files + str(x) + '.svg ' + UPLOAD_FOLDER)
staticString = Markup(staticString)
carouselstr = Markup(carouselstr)
carouselcap = Markup(carouselcap)
os.system("rm -r " + Name)
return render_template("results.html", carouselstr = carouselstr, \
carouselcap = carouselcap, staticString = staticString)