def drawPieChart(val1):
#To draw a pie chart
val2 = 100 - val1
chart = PieChart3D(250, 100)
chart.add_data([val1, val2])
chart.set_pie_labels(['Use', 'Not Use'])
print '<img src="%s"></img></td>' % chart.get_url()
def create_chart(tweet_dict):
# Calls to GoogleChart
chart=PieChart3D(500,200)
chart.add_data(tweet_dict.values())
chart.set_colours(['282D8F'])
chart.set_pie_labels(tweet_dict.keys())
return chart.get_url()
def pie_google(data, output):
from pygooglechart import PieChart3D
chart = PieChart3D(750, 400)
chart.add_data(data[1])
chart.set_pie_labels(data[0])
print chart.get_url()
chart.download(output)
def post(self):
value = self.request.get('slider')
rec = getRecords(value,str(self.session.get("cid")))
table = rec['records']
sum = rec['sum']
chart = PieChart3D(325, 100)
categoryvalues = []
for x in sum.values():
if x : categoryvalues.append(x)
chart.add_data(categoryvalues)
# Assign the labels to the pie data
categorykey=[]
for x in sum.keys():
if sum[x]: categorykey.append(x)
chart.set_pie_labels(categorykey)
totalSum = 0
for x in sum.values():
totalSum = totalSum + x
# Print the chart URL
pieURL = chart.get_url()
self.response.out.write(template.render('templates/analysisview/app.html',{
'pieURL':pieURL,
'descpie':'Relative Spendings',
'desctable':'Category Wise Spendings',
'total':totalSum,
'table':table,
}))
def get_piechart_url(self):
from pygooglechart import PieChart3D
#import pdb
#pdb.set_trace()
answer_set = self.answer_set.all()
chart = PieChart3D(500, 230)
chart.add_data([a.votes for a in answer_set])
chart.set_pie_labels([a.answer for a in answer_set])
return chart.get_url()
def get(self):
time1 = self.request.get('time')
if time1 == 'today':
sum = makeDailyPie(str(self.session.get("cid")))
table = makeDailyTable(str(self.session.get("cid")))
desctable ='All Spendings'
if time1 == 'week':
sum = makeWeekPie(str(self.session.get("cid")))
table = []
for x,y in sum.items():
table.append(userDB(amount = str(y),category = str(x)))
desctable = 'Category wise Spending'
if time1 == 'month':
sum = makeMonthPie(str(self.session.get("cid")))
table = []
for x,y in sum.items():
table.append(userDB(amount = str(y),category = str(x)))
desctable = 'Category wise Spending'
if time1 == 'year':
sum = makeYearPie(str(self.session.get("cid")))
table = []
for x,y in sum.items():
table.append(userDB(amount = str(y),category = str(x)))
desctable = 'Category wise Spending'
# Create a chart object of 250x100 pixels
chart = PieChart3D(325, 100)
# Add some data
categoryvalues = []
for x in sum.values():
if x : categoryvalues.append(x)
chart.add_data(categoryvalues)
# Assign the labels to the pie data
categorykey=[]
for x in sum.keys():
if sum[x]: categorykey.append(x)
chart.set_pie_labels(categorykey)
totalSum = 0
for x in sum.values():
totalSum = totalSum + x
# Print the chart URL
pieURL = chart.get_url()
self.response.out.write(template.render('templates/analysisview/app.html',{
'pieURL':pieURL,
'descpie':'Relative Spendings',
'desctable':desctable,
'total':totalSum,
'table':table,
}))
def hello_world():
# Create a chart object of 200x100 pixels
chart = PieChart3D(250, 100)
# Add some data
chart.add_data([20, 10])
# Assign the labels to the pie data
chart.set_pie_labels(['Hello', 'World'])
# Download the chart
chart.download('pie-hello-world.png')
def tipovidomejn_grafik():
"""Вкупно колку домејни има по типови"""
c2 = conn.cursor()
tipovi = {
'.com.mk': 0,
'.org.mk': 0,
'.gov.mk': 0,
'.name.mk': 0,
'.net.mk': 0,
'.inf.mk': 0,
'.edu.mk': 0
}
vchera = (datetime.datetime.now() - datetime.timedelta(1)).date()
# select count(distinct domen) from domaininfo where status = 'Y' //Broj na site domeni
#
c2.execute("select count(distinct domejn) from domejni where datum=?",
(vchera.strftime("%Y-%m-%d"), ))
vkupno = c2.fetchone()[0]
ostanati = 0
for tip, broj in tipovi.iteritems():
c2.execute(
"select count(distinct domejn) from domejni where datum=? and domejn like ?",
(vchera.strftime("%Y-%m-%d"), '%%%s' % tip))
tipovi[tip] = c2.fetchone()[0]
ostanati += tipovi[tip]
tipovi['.mk'] = vkupno - ostanati
chart = PieChart3D(500, 200)
chart.add_data([x for x in tipovi.itervalues()])
chart.set_pie_labels([
"%s (%s%%)" % (x, round(y * 100.0 / vkupno, 2))
for x, y in tipovi.iteritems()
])
chart.set_legend(["%s (%s)" % (x, y) for x, y in tipovi.iteritems()])
chart.set_legend_position('b')
chart.set_title("Вкупно %s .мк домени од кои:" % vkupno)
return chart.get_url()
def buildPieChart3D(self, data, addValueToLabel=False, sortByKeys=False):
chart = PieChart3D(self.defaultWidth, self.defaultHeight)
labels = list()
dataPoints = list()
keys = sorted(data.keys()) if sortByKeys else data.keys()
for key in keys:
value = data[key]
label = key
if addValueToLabel: label += ' (' + str(value) + ')'
labels.append(label)
dataPoints.append(value)
chart.add_data(dataPoints)
chart.set_pie_labels(labels)
return chart
def buildTagBuddiesChart(self, data):
if len(data) > 5:
data = data[:5]
bars = list()
labels = list()
for value in data:
bars.append(value[1])
labels.append(value[0] + ' (' + str(value[1]) + ')')
chart = PieChart3D(self.defaultWidth, self.defaultHeight)
chart.add_data(bars)
chart.set_pie_labels(labels)
chart.set_title('TOP 5 Tag Buddies')
return chart
def buildWallPostersChart(self, data):
if len(data) > 5:
data = data[:5]
values = list()
keys = list()
for value in data:
values.append(value[1])
keys.append(value[0] + ' (' + str(value[1]) + ')')
chart = PieChart3D(self.defaultWidth, self.defaultHeight)
chart.add_data(values)
chart.set_pie_labels(keys)
chart.set_title('Top 5 People Posting on Your Wall')
return chart
def buildTopRecordsPieChartFromSortedData(self, data, title):
if len(data) > 5:
data = data[:5]
values = list()
keys = list()
for value in data:
values.append(value[1])
keys.append(
self.removeNonAscii(value[0]) + ' (' + str(value[1]) + ')')
chart = PieChart3D(self.defaultWidth, self.defaultHeight)
chart.add_data(values)
chart.set_pie_labels(keys)
chart.set_title(title)
return chart
def group_membership_breakdown(request, group_slug):
group = get_object_or_404(BaseGroup, slug=group_slug)
statusBreakdownChart = PieChart3D(600, 240)
allusers = group.member_users.all().count()
regular = group.member_users.filter(
memberprofile__membership_expiry__gt=date.today()).count()
associate = group.get_accepted_members().count() - regular
mlist = allusers - regular - associate
statusBreakdownChart.add_data([
mlist +
1, # FIXME: the +1 is needed so pygoogle doesn't crash (it doesn't handle zeroes well)
associate + 1,
regular + 1
])
statusBreakdownChart.set_colours(['ff0000', 'ffff00', '00ff00'])
statusBreakdownChart.set_pie_labels(
["mailing list members", "associate members", "regular members"])
return statusBreakdownChart.get_url()
def stacked_vertical():
total = Totals.get_or_insert('total')
if len(total.shirts) == 0:
shirts = sorted(T_Shirts, key=lambda shirt: shirt[0])
for shirt in shirts:
total.shirts.append(shirt[0])
total.votes.append(0)
votes = []
shirts = []
i = 0
while i < len(total.votes):
if total.votes[i] != 0:
votes.append(total.votes[i])
shirts.append('Design %s' % total.shirts[i])
i += 1
if len(votes) == 0:
return ''
chart = PieChart3D(650, 300)
chart.add_data(votes)
chart.set_pie_labels(shirts)
return chart.get_url()
def main_dashboard(request):
today, created = DailyStats.objects.get_or_create(day=date.today())
if today.users == 0:
today.users = 1
# ---- Daily usage ----
enddate = date.today()
#startdate = enddate - timedelta(weeks=60)
startdate = enddate - timedelta(weeks=4)
averageusage = DailyStats.objects.filter(
day__range=(startdate, enddate)).order_by('day')
days = []
signins = []
posts = []
replies = []
whiteboards = []
signups = []
listsignups = []
listupgrades = []
deletions = []
numUsers = []
numRegularMembers = []
regupgrades = []
renewals = []
regdowngrades = []
for s in averageusage:
days.append(s.day.strftime("%B %y"))
signins.append(s.signins)
posts.append(s.posts)
replies.append(s.replies)
whiteboards.append(s.whiteboardEdits)
signups.append(s.signups)
listsignups.append(s.mailinglistsignups)
listupgrades.append(s.mailinglistupgrades)
deletions.append(s.deletions)
numUsers.append(s.users)
numRegularMembers.append(s.regularmembers)
regupgrades.append(s.regupgrades)
renewals.append(s.renewals)
regdowngrades.append(s.regdowngrades)
xaxis = []
#for i in range(0, len(days), 1): # this will make limited test data look better
for i in range(0, len(days), len(days) / 8):
xaxis.append(days[i])
# ---- Daily usage ----
dailyUsageChart = SimpleLineChart(600, 450, y_range=(0, max(signins)))
#chart.add_data(avgsignins)
dailyUsageChart.add_data(posts)
dailyUsageChart.add_data(replies)
dailyUsageChart.add_data(signins)
dailyUsageChart.add_data(whiteboards)
dailyUsageChart.set_colours(['ff0000', 'ffff00', '00ff00', '0000ff'])
dailyUsageChart.set_legend(['posts', 'replies', 'signins', 'whiteboards'])
dailyUsageChart.set_legend_position('b')
#yaxis = range(0, max_signins + 1, 2) # this will make limited test data look better
yaxis = range(0, max(signins), max(signins) / 10)
yaxis[0] = ''
dailyUsageChart.set_axis_labels(Axis.LEFT, yaxis)
dailyUsageChart.set_axis_labels(Axis.BOTTOM, xaxis)
dailyUsage = dailyUsageChart.get_url()
# ---- Account changes ----
accountChangesChart = SimpleLineChart(600, 450, y_range=(0, 25))
accountChangesChart.add_data(signups)
accountChangesChart.add_data(listsignups)
accountChangesChart.add_data(listupgrades)
accountChangesChart.add_data(deletions)
accountChangesChart.set_colours(['ff0000', 'ffff00', '00ff00', '0000ff'])
accountChangesChart.set_legend(
['account signups', 'email signups', 'email upgrades', 'deletions'])
accountChangesChart.set_legend_position('b')
#yaxis = range(0, 25, 2) # this will make limited test data look better
yaxis = range(0, min(max(listsignups), 10), max(max(listsignups) / 10, 1))
yaxis[0] = ''
accountChangesChart.set_axis_labels(Axis.LEFT, yaxis)
accountChangesChart.set_axis_labels(Axis.BOTTOM, xaxis)
accountChanges = accountChangesChart.get_url()
# ---- Membership ----
membershipChart = SimpleLineChart(600, 450, y_range=(42000, 52000))
membershipChart.add_data(numUsers)
membershipChart.add_data(numRegularMembers)
membershipChart.set_colours(['ff0000', '0000ff'])
membershipChart.set_legend(['total users', 'regular members'])
membershipChart.set_legend_position('b')
yaxis = range(42000, 52000, 1000)
yaxis[0] = ''
yaxis2 = range(0, 1500, 50)
yaxis2[0] = ''
membershipChart.set_axis_labels(Axis.LEFT, yaxis)
membershipChart.set_axis_labels(Axis.RIGHT, yaxis2)
membershipChart.set_axis_labels(Axis.BOTTOM, xaxis)
membershipChart = membershipChart.get_url()
# ---- Account changes ----
membershipChangesChart = SimpleLineChart(600, 450, y_range=(0, 10))
membershipChangesChart.add_data(regupgrades)
membershipChangesChart.add_data(renewals)
membershipChangesChart.add_data(regdowngrades)
membershipChangesChart.set_colours(['ff0000', 'ffff00', '00ff00'])
membershipChangesChart.set_legend(
['regular upgrades', 'renewals', 'regular downgrades'])
membershipChangesChart.set_legend_position('b')
#yaxis = range(0, 25, 2) # the same.
yaxis = range(
0, max(max(regupgrades), max(regdowngrades), max(renewals)),
max(max(max(regupgrades), max(regdowngrades), max(renewals)) / 10, 1))
yaxis[0] = ''
membershipChangesChart.set_axis_labels(Axis.LEFT, yaxis)
membershipChangesChart.set_axis_labels(Axis.BOTTOM, xaxis)
membershipChanges = membershipChangesChart.get_url()
# ---- Status breakdown ----
statusBreakdownChart = PieChart3D(600, 240)
mlistmembers = today.users - today.regularmembers - today.associatemembers
statusBreakdownChart.add_data([
mlistmembers +
1, # FIXME: the +1 is needed so pygoogle doesn't crash (it doesn't handle zeroes well)
today.associatemembers + 1,
today.regularmembers + 1
])
statusBreakdownChart.set_colours(['ff0000', 'ffff00', '00ff00'])
statusBreakdownChart.set_pie_labels(
["mailing list members", "associate members", "regular members"])
statusBreakdown = statusBreakdownChart.get_url()
# ---- Membership breakdown ----
chapters = Network.objects.filter(chapter_info__isnull=False,
is_active=True)
chapternames = []
chaptermembers = []
for chapter in chapters:
chapternames.append(chapter.slug)
chaptermembers.append(chapter.members.all().count())
membershipBreakdownChart = StackedHorizontalBarChart(
500, 500, x_range=(0, max(chaptermembers)))
membershipBreakdownChart.add_data(chaptermembers)
yaxis = range(0, max(chaptermembers), 10)
yaxis[0] = ''
membershipBreakdownChart.set_axis_labels(Axis.BOTTOM, yaxis)
membershipBreakdownChart.set_axis_labels(Axis.LEFT, chapternames)
membershipBreakdownChart.set_bar_width(330 / len(chapternames))
membershipBreakdown = membershipBreakdownChart.get_url()
# ---- Province breakdown ----
profiletype = ContentType.objects.get_for_model(MemberProfile)
addresses = Address.objects.filter(content_type=profiletype)
totalprov = Address.objects.filter(
content_type=profiletype).count() + 1 # FIXME
provinces = []
provincecount = []
provincelist = list(pycountry.subdivisions.get(country_code='CA'))
for p in provincelist:
pcode = p.code.split('-')[1]
provincecount2 = Address.objects.filter(content_type=profiletype,
province=pcode).count()
if provincecount2 == 0:
provincecount2 = 1
provincecount.append(provincecount2)
provinces.append(pcode + " (%d%%)" %
(provincecount2 * 100 / totalprov))
#provinces = sorted(provinces)
provinceBreakdownChart = PieChart3D(600, 240)
provinceBreakdownChart.add_data(provincecount)
#provinceBreakdownChart.set_colours(['ff0000', 'ffff00', '00ff00'])
provinceBreakdownChart.set_pie_labels(provinces)
provinceBreakdown = provinceBreakdownChart.get_url()
# ---- Gender breakdown ----
males = MemberProfile.objects.filter(gender='M').count() + 1
females = MemberProfile.objects.filter(gender='F').count() + 1
genderunknown = MemberProfile.objects.filter(
gender__isnull=True).count() + 1 #FIXME
gendertotal = males + females + genderunknown
genderBreakdownChart = PieChart3D(600, 240)
genderBreakdownChart.add_data([males, females, genderunknown])
genderBreakdownChart.set_colours(['ff0000', 'ffff00', '00ff00'])
genderBreakdownChart.set_pie_labels([
'Male (%d%%)' % (males * 100 / gendertotal),
'Female (%d%%)' % (females * 100 / gendertotal),
'Unspecified (%d%%)' % (genderunknown * 100 / gendertotal)
])
genderBreakdown = genderBreakdownChart.get_url()
# ---- Student breakdown ----
students = User.objects.filter(
studentrecord__graduation_date__isnull=True).count() + 1
nonstudents = User.objects.filter(
workrecord__end_date__isnull=True).count() + 1
# yeah, i know, not 100% accurate since a student can have a part-time job
studentBreakdownChart = PieChart3D(600, 240)
studentBreakdownChart.add_data([students, nonstudents])
studentBreakdownChart.set_colours(['ff0000', '00ff00'])
studentBreakdownChart.set_pie_labels(['Students', 'Non-students'])
studentBreakdown = studentBreakdownChart.get_url()
# ---- Language breakdown ----
preferen = MemberProfile.objects.filter(language='E').count() + 1
preferfr = MemberProfile.objects.filter(language='F').count() + 1
prefernone = MemberProfile.objects.filter(
language__isnull=True).count() + 1
languageBreakdownChart = PieChart3D(600, 240)
languageBreakdownChart.add_data([preferen, preferfr, prefernone])
languageBreakdownChart.set_colours(['ff0000', 'ffff00', '00ff00'])
languageBreakdownChart.set_pie_labels(
['english', 'french', 'not specified'])
languageBreakdown = languageBreakdownChart.get_url()
# ---- Post breakdown ----
postspublic = GroupTopic.objects.filter(
parent_group__visibility='E',
parent_group__parent__isnull=True).count() + 1
postsprivate = GroupTopic.objects.filter(
parent_group__parent__isnull=True).exclude(
parent_group__visibility='E').count() + 1
postspublicchapter = GroupTopic.objects.filter(
parent_group__visibility='E',
parent_group__parent__isnull=False).count() + 1
postsprivatechapter = GroupTopic.objects.filter(
parent_group__parent__isnull=False).exclude(
parent_group__visibility='E').count() + 1
postcount = postspublic + postsprivate + postspublicchapter + postsprivatechapter
postBreakdownChart = PieChart3D(600, 240)
postBreakdownChart.add_data(
[postspublic, postspublicchapter, postsprivatechapter, postsprivate])
#postBreakdownChart.set_colours(['ff0000', 'ffff00', '00ff00'])
postBreakdownChart.set_pie_labels(
['public', 'public chapter', 'private chapter', 'private'])
postBreakdown = postBreakdownChart.get_url()
# ---- Login distribution ----
logincount = []
malelogins = []
femalelogins = []
for i in range(0, 30):
logincount.append(
MemberProfile.objects.filter(login_count__gte=i).count())
malelogins.append(
MemberProfile.objects.filter(login_count__gte=i,
gender='M').count())
femalelogins.append(
MemberProfile.objects.filter(login_count__gte=i,
gender='F').count())
loginDistribution = SimpleLineChart(600, 450, y_range=(0, 9000))
loginDistribution.add_data(logincount)
loginDistribution.add_data(malelogins)
loginDistribution.add_data(femalelogins)
loginDistribution.set_colours(['ff0000', '0000ff', '00ff00'])
loginDistribution.set_legend(['logins', 'male', 'female'])
loginDistribution.set_legend_position('b')
yaxis = range(
0, 9000,
500) # that last number should be 25 or 50. but for testing...
yaxis[0] = ''
loginDistribution.set_axis_labels(Axis.LEFT, yaxis)
loginDistribution.set_axis_labels(Axis.BOTTOM, range(0, 30))
loginDistribution = loginDistribution.get_url()
# ---- Login recency ----
loginrecent = []
loginrecentdate = []
thedate = date(date.today().year - 1, date.today().month, 1)
skip = False
while thedate.year != date.today().year or thedate.month != date.today(
).month:
if thedate.month == 12:
enddate = date(year=thedate.year + 1, month=1, day=1)
else:
enddate = date(year=thedate.year, month=thedate.month + 1, day=1)
loginrecent.append(
MemberProfile.objects.filter(
previous_login__range=(thedate, enddate)).count())
if not skip:
loginrecentdate.append(thedate.strftime("%B %y"))
else:
loginrecentdate.append("")
skip = not skip
thedate = enddate
loginRecency = SimpleLineChart(600, 450, y_range=(0, max(loginrecent) + 1))
loginRecency.add_data(loginrecent)
yaxis = range(0, max(loginrecent), max(
max(loginrecent) / 10,
1)) # that last number should be 25 or 50. but for testing...
if len(yaxis) == 0:
yaxis.append(10)
yaxis.append(10)
yaxis[0] = ''
loginRecency.set_axis_labels(Axis.LEFT, yaxis)
loginRecency.set_axis_labels(Axis.BOTTOM, loginrecentdate)
loginRecency = loginRecency.get_url()
# ---- Age distribution ----
ages = []
for age in range(15, 75):
year = date.today().year - age
ages.append(
MemberProfile.objects.filter(date_of_birth__year=year).count())
ageDistribution = SimpleLineChart(600, 450, y_range=(0, max(ages) + 1))
ageDistribution.add_data(ages)
yaxis = range(0, max(ages) + 1, 50)
yaxis[0] = ''
ageDistribution.set_axis_labels(Axis.LEFT, yaxis)
ageDistribution.set_axis_labels(Axis.BOTTOM, range(15, 75, 5))
ageDistribution = ageDistribution.get_url()
# ---- Finally! ----
return render_to_response(
"stats/dashboard.html", {
"signins": today.signins,
"posts": today.posts,
"replies": today.replies,
"signups": today.signups,
"listsignups": today.mailinglistsignups,
"listupgrades": today.mailinglistupgrades,
"deletions": today.deletions,
"regupgrades": today.regupgrades,
"regdowngrades": today.regdowngrades,
"renewals": today.renewals,
"totalusers": today.users,
"dailyUsage": dailyUsage,
"accountChanges": accountChanges,
"membershipChart": membershipChart,
"membershipChanges": membershipChanges,
"statusBreakdown": statusBreakdown,
"mlistmembers": mlistmembers,
"mlistmemberspercent": mlistmembers * 100 / today.users,
"associatemembers": today.associatemembers,
"associatememberspercent":
today.associatemembers * 100 / today.users,
"regularmembers": today.regularmembers,
"regularmemberspercent": today.regularmembers * 100 / today.users,
"membershipBreakdown": membershipBreakdown,
"provinceBreakdown": provinceBreakdown,
"provincecount": totalprov,
"genderBreakdown": genderBreakdown,
"studentBreakdown": studentBreakdown,
"languageBreakdown": languageBreakdown,
"postBreakdown": postBreakdown,
"loginDistribution": loginDistribution,
"loginRecency": loginRecency,
"ageDistribution": ageDistribution
},
context_instance=RequestContext(request))
def python_pie3D():
chart = PieChart3D(250, 250)
chart.add_data([100, 200, 250, 500, 900])
chart.set_pie_labels("Anuj Sid Nikunj Kardam Maru".split())
print chart.get_url()
chart.download("hisab.png")
large_digit = sorted(number, reverse=True)
small_combained = int(''.join(small_digit))
large_combained = int(''.join(large_digit))
kc = large_combained - small_combained
number = map(lambda x: x, str(kc).zfill(4))
iter = iter + 1
fd[x] = iter
for k, v in fd.iteritems():
print k,
print 'takes',
print v,
print 'iterations to reach 6174'
gm.append(v)
sm = (Counter(gm).items())
sm = sorted(sm)
print 'Iteration Total Count of Numbers'
for i in range(len(sm)):
xx.append(str(sm[i][0]) + ' iterations')
yy.append(sm[i][1])
print sm[i][0], #printing the no. of iterations
print '\t\t',
print sm[i][1]
#creating graph
chart = PieChart3D(500, 200)
chart.add_data(yy)
chart.set_pie_labels(xx)
chart.download('iter_pie_chart.png')
webbrowser.open(
'iter_pie_chart.png', new=0
) #Displays the graph in default browser appropriate to the callers environment.
raw_input("Press Enter to continue...")
def create_summary(first, amosbnk, prefix, ref_asm, utils, img, rund, nLibs,
taxa_level, dbdir):
#if __name__ == "__main__":
# if len(sys.argv) < 5:
# print "usage: create_report.py <metaphyler tab file> <AMOS bnk> <output prefix> <ref_asm> <Utils dir> <run dir> <# of libs> <taxa level of classifications>"
# sys.exit(0)
html_prefix = prefix
prefix = prefix.replace("/html/", "")
MA_dir = prefix
MA_dir = MA_dir.replace("/Postprocess/out", "")
mp = open(first, 'r')
#mp2 = open(sys.argv[1].replace("s12","s3"),'r')
# set working dir
os.chdir(html_prefix)
if not os.path.exists(html_prefix + "asmstats.out"):
libPath = rund.rsplit(os.sep, 1)[0] + os.sep + rund.rsplit(
os.sep, 1)[-1].replace("bin", "lib")
#print "perl -I %s %s/perl/statistics.pl %s > %sasmstats.out"%(libPath,utils,ref_asm,html_prefix)
run_process(
_settings, "perl -I %s %s/perl/statistics.pl %s > %sasmstats.out" %
(libPath, utils, ref_asm, html_prefix), "Postprocess")
report = open(html_prefix + "asmstats.out", 'r')
initialStep = "Classify"
# get metamos version
version = "1.0"
summary = open("%s/pipeline.run" % (MA_dir), 'r')
for line in summary:
line = line.replace("\n", "")
if "#" in line:
continue
elif "metAMOS Version:" in line:
version = line.replace("\n", "").split("\t")[-1]
summary.close()
steps = []
steps.append("Preprocess")
steps.append("Assemble")
steps.append("MapReads")
steps.append("Validate")
#steps.append("MultiAlign")
steps.append("FindORFS")
steps.append("FindRepeats")
steps.append("Scaffold")
steps.append("FindScaffoldORFS")
steps.append("Abundance")
steps.append("Classify")
steps.append("FunctionalAnnotation")
steps.append("Propagate")
steps.append("Bin")
steps.append("Browse Results")
step_status = {}
step_status["Preprocess"] = "OK"
step_status["Assemble"] = "OK"
step_status["MapReads"] = "OK"
step_status["Validate"] = "OK"
#step_status["MultiAlign"] = "OK"
step_status["FindORFS"] = "OK"
step_status["FindRepeats"] = "OK"
step_status["Scaffold"] = "OK"
step_status["FindScaffoldORFS"] = "OK"
step_status["Abundance"] = "FAIL"
step_status["Classify"] = "FAIL"
step_status["FunctionalAnnotation"] = "FAIL"
step_status["Propagate"] = "NONE"
step_status["Bin"] = "NONE"
step_status["Browse Results"] = "OK"
##get status of each step from Log dir
for step in steps:
if step == "Browse Results":
continue
stepn = step.lower()
started = False
completed = False
skipped = False
if os.path.exists("%s/Logs/%s.started" % (MA_dir, stepn)):
started = True
if os.path.exists("%s/Logs/%s.ok" % (MA_dir, stepn)):
completed = True
if os.path.exists("%s/Logs/%s.skip" % (MA_dir, stepn)):
skipped = True
if completed and not skipped:
step_status[step] = "OK"
elif skipped:
step_status[step] = "SKIP"
elif started and not completed:
step_status[step] = "FAIL"
elif not started:
step_status[step] = "NONE"
else:
step_status[step] = "NONE"
#+male1 /cbcb/project-scratch/sergek/metAMOS/individualAsms/m1_asm proba b- metaphyler=1
## call Dan's script, for now on a single sample/run
cpfile = open("%s/plot.tab" % (html_prefix), 'w')
cpfile.write("+sample1\t%s\tproba\tb-\tmetaphyler=1\n" % (MA_dir))
cpfile.close()
#os.system("python %s/python/create_plots.py %s/plot.tab proba1"%(utils,html_prefix))
if _havePlots:
create_plots("%s/plot.tab" % (html_prefix), "%s" % ("proba1"))
##update counts
#count reads
os.system(
"cat `ls %s/Preprocess/out/* |egrep 'lib[0-9]*\.fasta$'` | grep -c \">\" > readcount.txt"
% (MA_dir))
readcount = open("readcount.txt", 'r').read().replace("\n", "")
#print readcount
os.system("rm readcount.txt")
#count contigs
os.system(
"grep -c \">\" %s/Assemble/out/proba.asm.contig > contigcount.txt" %
(MA_dir))
contigcount = open("contigcount.txt", 'r').read().replace("\n", "")
#print contigcount
os.system("rm contigcount.txt")
#count scaffolds
os.system(
"grep -c \">\" %s/Scaffold/out/proba.scaffolds.final > scafcount.txt" %
(MA_dir))
scaffoldcount = open("scafcount.txt", 'r').read().replace("\n", "")
#print scaffoldcount
os.system("rm scafcount.txt")
#count scaffolds
os.system("grep -c \">\" %s/Scaffold/out/proba.motifs > motifcount.txt" %
(MA_dir))
motifcount = open("motifcount.txt", 'r').read().replace("\n", "")
#print motifcount
os.system("rm motifcount.txt")
#count ORFs
os.system("grep -c \">\" %s/FindORFS/out/proba.fna > orfcount.txt" %
(MA_dir))
orfcount = open("orfcount.txt", 'r').read().replace("\n", "")
#print orfcount
os.system("rm orfcount.txt")
##copy stuff
for step in steps:
# step = step.lower()
if os.path.exists("%s/javascript/%s.html" % (utils, step)):
os.system("cp %s/javascript/%s.html %s/" %
(utils, step, html_prefix))
os.system("cp %s/Logs/COMMANDS.log %s/pipeline.commands" %
(MA_dir, html_prefix))
os.system("cp %s/pipeline.run %s/pipeline.summary" % (MA_dir, html_prefix))
os.system("cp %s/javascript/style.css %s/" %
(utils, html_prefix)) # TEMP: change back to cp
os.system("cp -r %s/../KronaTools/src %s/../KronaTools/img %s/" %
(utils, utils, html_prefix)) # TODO: unhack KronaTools path
# os.system("cp %s/blocks.jpg %s/"%(img,html_prefix))
# os.system("cp %s/blocks_small.jpg %s/"%(img,html_prefix))
os.system("cp %s/blocks_dark_tiny.png %s/" % (img, html_prefix))
os.system("cp %s/name.png %s/" % (img, html_prefix))
# generate dynamic java scripts
# first classify and propagate
#os.system("python %s/python/get_classify_stats.py %s/propagate.in.clusters %s/propagate.out.clusters %s/DB/tax_key.tab %s Classify.html Propagate.html %s"%(utils, html_prefix, html_prefix, utils, html_prefix, taxa_level))
get_classify_stats("%s/propagate.in.clusters" % (html_prefix),
"%s/propagate.out.clusters" % (html_prefix),
"%s/tax_key.tab" % (dbdir), "%s" % (html_prefix),
"Bin.html", "Propagate.html", "%s" % (taxa_level))
# generate preprocess
preprocess = markup.page()
preprocess.init(css="style.css") #bodyattrs={'style':"margin:0px"})
preprocess.p()
nQC = 0
for i in range(1, nLibs + 1):
if os.path.exists("%s/lib%d.1.fastqc/fastqc_report.html" %
(html_prefix, i)):
nQC = nQC + 1
summary = open("%s/pipeline.ini" % (MA_dir), 'r')
libcnt = 1
format = None
mmin = 0
mmax = 0
mated = False
interleaved = False
innie = False
linkerType = ""
libadded = False
firstLib = True
headerArray = []
dataArray = []
for line in summary:
line = line.replace("\n", "")
if "#" in line:
continue
elif "asmcontigs:" in line:
asmc = line.replace("\n", "").split("\t")[-1]
if len(asmc) <= 2:
continue
preprocess.add(
"<div class=\"datagrid\">Pre-assembled contigs input: %s</div>"
% (asmc))
preprocess.br()
elif "format:" in line:
if format and not libadded:
outputLibraryInfo(headerArray, dataArray, firstLib, libcnt,
format, mated, interleaved, mmin, mmax,
nQC > 0)
libcnt += 1
libadded = False
format = line.replace("\n", "").split("\t")[-1]
elif "mated:" in line:
mated = str2bool(line.replace("\n", "").split("\t")[-1])
elif "innie:" in line:
innie = str2bool(line.replace("\n", "").split("\t")[-1])
elif "linker:" in line:
linkerType = line.replace("\n", "").split("\t")[-1]
elif "interleaved:" in line:
interleaved = str2bool(line.replace("\n", "").split("\t")[-1])
elif "f1:" in line:
data = line.split("\t")
inf = data[1].split(",")
mmin = int(inf[1])
mmax = int(inf[2])
elif "f2:" in line:
data = line.split("\t")
inf = data[1].split(",")
mmin = int(inf[1])
mmax = int(inf[2])
elif "frg" in line:
data = line.split("\t")
if format and not libadded:
outputLibraryInfo(headerArray, dataArray, firstLib, libcnt, format,
mated, interleaved, mmin, mmax, nQC > 0)
preprocess.add(getTable(headerArray, dataArray))
summary.close()
if os.path.exists("%s/Postprocess/out/html/kmergenie_report.html" %
(MA_dir)):
preprocess.iframe(id_="KmerGenie",
src_="kmergenie_report.html",
width="800",
height="5000")
preprocess_out = open("%s/Preprocess.html" % (html_prefix), 'w')
preprocess_out.write(preprocess.__str__())
preprocess_out.close()
validate_out = open("%s/Validate.html" % (html_prefix), 'w')
validate = markup.page()
validate.init(css="style.css",
bodyattrs={'style': "background-color:#FFFFFF;"})
headerArray = []
dataArray = []
firstScore = True
bestAsm = ""
refs = []
if os.path.exists("%s/Postprocess/out/asm.scores" % (MA_dir)):
best = open("%s/Postprocess/out/best.asm" % (MA_dir), 'r')
bestAsm = best.read()
best.close()
laps = open("%s/Postprocess/out/asm.scores" % (MA_dir), 'r')
validate.p()
validate.add("<div class=\"datagrid\">")
validate.add("Selected assembler: %s" % (bestAsm))
ref = open("%s/Postprocess/out/ref.name" % (MA_dir), 'r')
first = True
for r in ref.xreadlines():
refs.append(r)
if first:
validate.br()
first = False
validate.add("Selected reference: %s" % (r))
ref.close()
if os.path.exists("%s/Bin/out/contaminant.true" % (MA_dir)):
cont = open("%s/Bin/out/contaminant.true" % (MA_dir), 'r')
contPercent = cont.read().split()
cont.close()
validate.br()
validate.add(
"<b>Sample may have contaminants, only %s%% contigs/reads >%sbp assigned to %s. Check Classify output</b>"
% (contPercent[0], contPercent[2], contPercent[1]))
validate.br()
for line in laps:
line = line.replace("\n", "")
if "#" in line:
continue
else:
res = line.split("\t")
outputValidate(headerArray, dataArray, firstScore, bestAsm,
res)
firstScore = False
validate.add(getTable(headerArray, dataArray))
validate.add("</div>")
laps.close()
# when we have quast, we will add our table to their report, otherwise write standalone report
if os.path.exists(
"%s/Postprocess/out/html/quast/combined_quast_output/report.html" %
(MA_dir)):
os.system(
"cp %s/Postprocess/out/html/quast/combined_quast_output/report.html %s/Postprocess/out/html/quast/combined_quast_output/~report.html"
% (MA_dir, MA_dir))
quastIn = open(
"%s/Postprocess/out/html/quast/combined_quast_output/~report.html"
% (MA_dir), 'r')
quastOut = open(
"%s/Postprocess/out/html/quast/combined_quast_output/report.html" %
(MA_dir), 'w')
skip = False
output = False
for line in quastIn.xreadlines():
if not skip:
quastOut.write(line.strip().replace("<br>", "") + "\n")
elif output:
quastOut.write("margin-left: 50px;\n")
quastOut.write("padding-top: 10px;\n")
quastOut.write("background: #ffffff;\n")
output = False
if ".content" in line:
skip = True
output = True
elif "clear:" in line:
quastOut.write(line.strip() + "\n")
skip = False
output = False
quastIn.close()
quastOut.close()
validate.iframe(id_="quast",
src_="quast/combined_quast_output/report.html",
width="800",
height="1000")
validate_out.write(validate.__str__())
validate_out.close()
# multialign step
treeScripts = {}
treeScripts[
"http://www.jsphylosvg.com/js/jquery/jquery-1.4.2.min.js"] = "javascript"
treeScripts[
"http://www.jsphylosvg.com/js/jquery/jquery.simplemodal.1.4.1.min.js"] = "javascript"
treeScripts[
"http://www.jsphylosvg.com/js/raphael/raphael-min.js"] = "javascript"
treeScripts[
"http://www.jsphylosvg.com/js/jsphylosvg-min.js?1.29"] = "javascript"
treeScripts[
"http://www.jsphylosvg.com/js/unitip/js/unitip.js"] = "javascript"
treeScript = []
treeScript.append("<script type=\"text/javascript\">")
treeScript.append(
" var dataObject = { newick: '(M_canettii_CIPT_d:0.059437,(M_canettii_CIPT_e:0.07845,((((M_africanum_GM04118:0.00646,(M_bovis_AF2122_97:0.00269,(M_bovis_BCG_Tokyo_1:0.00013,((M_bovis_BCG_Korea_1:0.0,M_bovis_BCG_Pasteur:0.0):0.00014,M_bovis_BCG_Mexico:0.00013):0.00014):0.00294):0.00514):0.00207,(((MTBC_Beijing_NITR20:0.00914,(MTBC_CCDC5180:0.00102,(MTBC_CCDC5079:0.00423,MTBC_CCDC5079:0.00014):0.00078):0.00016):0.00368,((((MTBC_Erdman_ATCC_35:0.00075,MTBC:0.00123):0.00129,(MTBC_CDC1551:0.00245,MTBC_Haarlem3_NITR2:0.01398):0.00093):0.00065,((((MTBC_CTRI_2:0.001,(MTBC_KZN_4207:0.00014,(MTBC_KZN_605:0.00012,MTBC_KZN_1435:0.00014):0.00012):0.00071):0.00061,(MTBC_RGTB327:0.00462,MTBC_UT205:0.0012):0.00037):0.00014,MTBC_F11:0.00158):0.00109,(MTBC_H37Ra:0.00016,(MTBC_H37Rv:0.00028,MTBC_H37Rv:0.00014):0.00014):0.00281):0.00047):0.00112,MTBC_CAS_NITR204:0.009827):0.00022):0.00247,((MTBC_EAI5:0.0023,MTBC_EAI5_NITR206:0.00933):0.0035,(MTBC_RGTB423:0.00868,spades.45.asm.contig:0.0035):0.00066):0.00289):0.00015):0.07224,(M_canettii_CIPT_a:0.01891,M_canettii_CIPT_b:0.05096):0.03720):0.03909,M_canettii_CIPT_c:0.056869):0.00469):0.02099);' };"
)
treeScript.append(" function load() {")
treeScript.append(" var divVal = $('#svgCanvas').empty();")
treeScript.append(
" var isCircular = $('#circularize-value')[0].value;")
treeScript.append(
" Smits.PhyloCanvas.Render.Parameters.Rectangular.bufferX = 150;")
treeScript.append(
" Smits.PhyloCanvas.Render.Parameters.Circular.bufferRadius = 0.35;"
)
treeScript.append(
" Smits.PhyloCanvas.Render.Style.line.stroke = 'rgb(0,0,255)';")
treeScript.append(
" Smits.PhyloCanvas.Render.Style.text[\"font-size\"] = 10;")
treeScript.append(" if (isCircular.toLowerCase() == 'true') {")
treeScript.append(" phylocanvas = new Smits.PhyloCanvas(")
treeScript.append(" dataObject,")
treeScript.append(" 'svgCanvas',")
treeScript.append(
" 1000, 1000, 'circular'")
treeScript.append(" );")
treeScript.append(" $('#circularize-value')[0].value = 'false';")
treeScript.append(" } else {")
treeScript.append(" phylocanvas = new Smits.PhyloCanvas(")
treeScript.append(" dataObject,")
treeScript.append(" 'svgCanvas',")
treeScript.append(" 500, 500")
treeScript.append(" );")
treeScript.append(" $('#circularize-value')[0].value = 'true';")
treeScript.append(" }")
treeScript.append(" init();")
treeScript.append(" }")
treeScript.append("function snapshot() {")
treeScript.append(" var svgSource = phylocanvas.getSvgSource();")
treeScript.append(" if(svgSource) {")
treeScript.append(" var url = 'data:image/svg+xml,' + svgSource")
treeScript.append(" window.open(url);")
treeScript.append(" }")
treeScript.append(" }")
treeScript.append("</script>")
treeBody = {}
treeBody["onload"] = "load()"
maStep = markup.page()
maStep.add("\n".join(treeScript))
maStep.init(
css=("http://www.jsphylosvg.com//js/yui/build/cssfonts/fonts-min.css",
"http://www.jsphylosvg.com/js/unitip/css/unitip.css"),
script=treeScripts,
bodyattrs=treeBody)
maStep.div()
maStep.add(
"<input type=\"button\" id=\"download-link\" onclick=\"snapshot()\" value=\"Snapshot\" />"
)
maStep.div.close()
maStep.div()
maStep.add(
"<input type=\"button\" id=\"circularize-link\" onclick=\"load()\" value=\"Toggle Circular\" />"
)
maStep.add(
"<input type=\"hidden\" id=\"circularize-value\" value=\"false\">")
maStep.div.close()
maStep.div(id_="svgCanvas")
maStep.div.close()
maStep_out = open("%s/MultiAlign.html" % (html_prefix), 'w')
maStep_out.write(maStep.__str__())
maStep_out.close()
# todo, need to add report for MapReads including # reads mapped (%), contig coverage histogram, and % reads between contigs and number of links histogram. Also re-estimated insert sizes for each lib
#mapreads = markup.page()
#mapreads.init(bodyattrs={'style':"margin:0px"})
#mapreads.img(src_="hist_ctgcvg.png",height_="100%",width_="100%")
#mapreads_out = open("%s/MapReads.html"%(html_prefix), 'w')
#mapreads_out.write(mapreads.__str__())
##This will create ScaffoldSizes.png,ContigSizes.png
##create code to automatically generate .js files for HTML report
## let's start with Abundance
#abundance_js = open(html_prefix+"abundance.js",'w')
rdata = []
for line in report:
rdata.append(line)
if not os.path.exists(html_prefix + "covstats.out"):
run_process(
_settings, "%s/analyze-read-depth -x 2 %s > %scovstats.out" %
(rund, amosbnk, html_prefix), "Postprocess")
ff = open(html_prefix + "covstats.out", 'r')
covdata = []
#covdata = ff.readlines()
#zflag = 0
for line in ff:
covdata.append(line)
if not os.path.exists(html_prefix + "stats.out"):
if os.path.getsize("%s/Assemble/out/proba.asm.contig" % (MA_dir)) == 0:
run_process(_settings, "touch %sstats.out" % (html_prefix),
"Postprocess")
else:
#os.system("%s/astats %s > %sstats.out"%(rund,amosbnk,html_prefix))
run_process(
_settings,
"%s/astats %s > %sstats.out" % (rund, amosbnk, html_prefix),
"Postprocess")
dd = open(html_prefix + "stats.out", 'r')
ddata = dd.readlines()
ddf = ""
bflag = 0
cflag = 0
rflag = 0
for line in ddata:
if "<body>" in line:
bflag = 1
ddf += "<table border=\"1\">"
elif "[Contigs]" in line:
cflag = 1
ddf += line
elif "[Small" in line:
cflag = 0
elif "[Big" in line:
cflag = 0
elif "[Reads]" in line:
rflag = 1
ddf += line
elif cflag != 0 or rflag != 0:
if "N50" not in line:
ddf += line
else:
continue
mp.readline()
cov = []
abund = []
ids = []
mpd = mp.readlines()
phylum = False
for line in mpd:
if ">phylum" in line:
phylum = True
if len(line) < 3:
continue
data = line.split("\t")
if len(data) < 2:
continue
if not phylum:
continue
ids.append(data[0])
#cov.append(int(float(data[2])))
abund.append(100 * float(data[1]))
# Create a chart object of 200x100 pixels
# chart2 = StackedVerticalBarChart(600, 300)
chart2 = PieChart3D(550, 300)
chart2.set_colours(["0A8C8A", "EBB671", "DE091A"])
# Add some data
chart2.add_data(abund)
# chart2.add_data(abund2)
# Assign the labels to the pie data
chart2.set_pie_labels(ids)
# chart2.set_axis_labels(Axis.BOTTOM, ids)
# Download the chart
try:
chart2.download(html_prefix + 'abund.png')
except:
print "Warning: could not download abund.png"
chart = GroupedHorizontalBarChart(600, 500, x_range=(0, 100))
chart.set_bar_width(30)
chart.set_colours(("FF0000", "0000FF"))
#chart.set_colours_within_series(("FF0000","FF7F00","FFFF00","00FF00","0000FF","8B00FF","FFFFFF"))
# chart.set_colours(['00ff00', 'ff0000'])
chart.add_data(abund)
#chart.add_data(abund2)
#chart.add_data([1,4,9,16,25])
#category = ["even","staggered"]
#chart.set_legend(category)
ids = ids[::-1]
chart.set_axis_labels(Axis.LEFT, ids)
chart.set_axis_labels(Axis.BOTTOM,
[0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100])
#chart.set_axis_labels(Axis.LEFT, ["0)
index = chart.set_axis_labels(Axis.BOTTOM, ['Abundance (%)'])
chart.set_axis_style(index, '202020', font_size=10, alignment=0)
chart.set_axis_positions(index, [50])
index = chart.set_axis_labels(Axis.LEFT, ['Phylum'])
chart.set_axis_style(index, '202020', font_size=10, alignment=0)
chart.set_axis_positions(index, [50])
try:
chart.download(html_prefix + 'bar-phylum.png')
except:
print "Warning: could not download bar-phylum.png"
dt = datetime.now()
ds = dt.strftime("%d %b %Y,<br/>%l:%M%p")
title = "metAMOS report"
# header is blank for now
header = []
# write the javascript we need on the page
script = []
script.append("<script type=\"text/javascript\">")
script.append("var steps = ['%s'];" % ("','".join(steps)))
script.append("function load(step) {")
for step in steps:
if step_status[step] != "OK":
script.append(
" if (step.toLowerCase() == \"%s\".toLowerCase()) {" %
(step))
script.append(" return;")
script.append(" }")
script.append(" for (var i = 0; i < steps.length; i++) {")
script.append(" var current = steps[i].toLowerCase();")
script.append(" if (current == step) {")
script.append(
" document.getElementById(step + 'Button').className = 'menuItemSelected';"
)
script.append(
" document.getElementById(step).style.display = 'block';")
script.append(
" document.getElementById(step + 'Marker').className = 'markerSelected';"
)
script.append(" } else {")
script.append(
" document.getElementById(current + 'Button').className = 'menuItemUnselected';"
)
script.append(
" document.getElementById(current).style.display = 'none';")
script.append(
" document.getElementById(current + 'Marker').className = 'markerUnselected';"
)
script.append(" }")
script.append(" }")
script.append("}")
script.append("")
script.append("</script>")
#<link rel="shortcut icon" href="../assets/ico/favicon.ico">
#<link rel="apple-touch-icon-precomposed" sizes="144x144" href="../assets/ico/apple-touch-icon-144-precomposed.png">
#<link rel="apple-touch-icon-precomposed" sizes="114x114" href="../assets/ico/apple-touch-icon-114-precomposed.png">
#<link rel="apple-touch-icon-precomposed" sizes="72x72" href="../assets/ico/apple-touch-icon-72-precomposed.png">
#<link rel="apple-touch-icon-precomposed" href="../assets/ico/apple-touch-icon-57-precomposed.png">
# generate the dictionary of javascript pages we need
scripts = {}
# scripts["file://%s/javascript/jquery-latest.js"%(utils)] = "javascript"
# scripts["http://code.jquery.com/jquery-latest.js"] = "javascript"
# now a javascript for each page
for step in steps:
scripts["%s.js" % (step.lower())] = "javascript"
# attributes for the body tax
body = {}
body["onload"] = "load('%s')" % (initialStep.lower())
# the footer for the page
footer = "" #"Generated %s"%(ds)
#styles = ( 'style2.css')#'./html/bootstrap.css', './html/boostrap-responsive.css')#'style2.css')#'layout.css', 'alt.css', 'images.css' )
#styles = ( 'layout.css', 'alt.css', 'images.css' )
#meta = ('viewport':"width=device-width, initial-scale=1.0",'description':'','author':'')
# create HTML page
page = markup.page()
# add the javascript free form
page.add("\n".join(script))
# initialize the rest of the body/html headers
page.init( title=title, \
css='style.css', \
script=scripts,\
header='\n'.join(header), \
bodyattrs=body, \
footer=footer )
# page.br()
#page.div( class_ = 'navbar navbar-fixed-top')
#page.div( class_ = 'navbar-inner')
#page.div( class_ = 'container', style_='width:100%;height=100%')
#page.div.close()
#page.div.close()
#page.div.close()
#page.div( id_='page' )
# header
# page.add('<table style="width:100%;"><tr><td><img src="blocks_small.jpg"/></td><td><a target="_blank" href="https://github.com/treangen/metAMOS/wiki"><div><img src="name.jpg"/><br/>Under peer review</a></div></td><td class="title" style="width:100%"></td></tr></table>')
'''
page.div( id_='header', style="background-color:#B8B8B8;clear:both;text-align:center;width:100%;height:7%;border:1px solid black")
page.h1("<u>MetAMOS <font color=\"blue\">v1.0</font> metagenomic assembly & analysis report</u>" , style_="text-align:center;vertical-align:top")
page.h1.close()
#page.div( id_='title')# style="vertical-align:bottom;")
#page.font( size=14)
#page.br( )
page.div.close()
'''
#<frameset rows="40%,60%"cols="80%,20%">
#<frame src="report.krona.html">
#<frameset rows="20%,20%">
#<frame src="report.krona.html">
#<frame src="report.krona.html">
#</frameset>
#<frameset rows="60%" cols="40%,40%">
#<frame src="report.krona.html">
#<frame src="report.krona2.html">
#</frameset>f
#<frameset rows="20%,20%,20%" cols="20%">
#<frame src="report.krona.html">
#<frame src="report.krona.html">
#<frame src="report.krona.html">
#</frameset>
#</frameset>
#</html>
#font, estimate
#page.div.close()
#page.frameset( rows_="40%,60%", cols_ = "80%,20%")
#page.div()
page.table(style_="width:100%;height:100%;")
page.tr()
page.td(id_="menu", style_="padding:0px;")
page.div(style_="height:100%;")
# page.table(style_="height:100%")
# page.tr()
# page.td()#style_="border-right:1px solid black")
# page.div(style_="box-shadow:inset -1px -1px 5px #555555;")
page.add(
"<a target=\"_blank\" href=\"https://github.com/treangen/metAMOS/wiki\"><img style=\"padding-top:5px;\" src=\"name.png\"/>"
)
page.add("<img src=\"blocks_dark_tiny.png\"/></a>")
# page.add("<img src=\"blocks_tiny2.jpg\"/>")
page.add(
"<div style=\"padding:2px;font-size:12px;\"><a target=\"_blank\" href=\"http://genomebiology.com/2013/14/1/R2\">Treangen TJ, Koren S, et. al. Genome Biol. 2013 Jan 15;14(1):R2. PMID: 23320958.</a></div>"
)
page.add("<br/>")
# page.div.close()
# page.td.close()
# page.tr.close()
#items = ["<a href=\"http://cbcb.umd.edu/software/metamos\">metAMOS website</a>", ]
#page.ul()
# page.tr()
# page.td(style_="padding:0px;")
page.table(id_="links", class_="menu")
for step in steps:
page.tr()
status = "NA"
try:
if step_status[step] == "OK":
status = "OK"
elif step_status[step] == "FAIL":
status = "FAIL"
elif step_status[step] == "SKIP":
status = "SKIPPED"
except KeyError:
continue
tableHTML = []
tableHTML.append(
"<td class=\"menuItemTd\"><a class=\"menuLink\" href=\"javascript:void(0)\"><div class=\"menuItem %s\"><div id=\"%sButton\" class=\"menuItemUnselected\" onclick=\"load('%s');\">"
% (status.lower(), step.lower(), step.lower()))
tableHTML.append(
"<table style='width:100%%;'><tr><td style='width:100%%;'><span class='step %sText'>%s</span>"
% (status.lower(), step))
tableHTML.append("<br>")
tableHTML.append(
"<span class='status %sText'>%s</span></td></tr></table>" %
(status.lower(), status))
tableHTML.append(
"</div></div></a></td><td><div id='%sMarker' class='markerUnselected'>●</div></td>"
% (step.lower()))
page.add("\n".join(tableHTML))
page.tr.close()
page.table.close()
# page.td.close()
# page.tr.close()
#page.ul.close()
# page.tr()
# page.td(style_="height:100%;")#border-right:1px solid black")
page.div(class_="notes")
page.add(
"<div style=\"font-size:14px;\"><br/><a target=\"_blank\" href=\"pipeline.summary\">Pipeline summary</a><br/>"
)
page.add(
"<a target=\"_blank\" href=\"pipeline.commands\">Run commands</a><br/><br/></div>"
)
tableHTML = []
tableHTML.append("<table style=\"font-size:12px\"><tr>")
tableHTML.append("<tr><td>Version:</td><td>%s</td></tr>" % (version))
tableHTML.append("<tr><td>Created:<br/> </td><td>%s</td></tr>" % (ds))
tableHTML.append("</table>")
page.add("\n".join(tableHTML))
page.div.close()
# page.td.close()
# page.tr.close()
# page.table.close()
page.div.close()
page.td.close()
page.td(id_="krona", style_="width:100%;height:100%padding:0px;")
page.table(class_="charts", style_="width:100%;height:100%")
page.tr()
page.td(class_="main", style_="height:100%", colspan_="4")
page.div(class_="shadow")
page.table(style_="width:100%;height:100%")
page.tr()
page.td(class_="corner")
page.td.close()
page.td()
page.td.close()
page.td(class_="corner")
page.td.close()
page.tr.close()
page.tr()
page.td()
page.td.close()
page.td(class_="inset")
for step in steps:
if step == "Browse Results":
page.iframe(id_=step.lower(), src_="../.", style_="display:none;")
else:
page.iframe(id_=step.lower(),
src_="%s.html" % (step),
style_="display:none;")
page.iframe.close()
page.td.close()
page.td()
page.td.close()
page.tr.close()
page.tr()
page.td(class_="corner")
page.td.close()
page.td()
page.td.close()
page.td(class_="corner")
page.td.close()
page.tr.close()
page.table.close()
page.div.close()
page.td.close()
page.tr.close()
#page.tr()
#page.div(id_="sideplots")#, style_="background-color:#FFFFFF;width:20.5%%;height:88%%;float:right;border:1px")
#page.div(id_="sideplot1", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.td(style_="width:25%")
#page.img(class_="chart", src_="ContigSizes.png")
#page.td.close()
#page.td(style_="width:25%")
#page.div.close()
#page.div(id_="sideplot2", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.img(class_="chart", src_="hist_contigs.png")
#page.td.close()
#page.td(style_="width:25%")
#page.div.close()
#page.div(id_="sideplot3", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.img(class_="chart", src_="ScaffoldSizes.png")
#page.td.close()
#page.td(style_="width:25%")
#page.div.close()
#page.div(id_="sideplot4", style_="background-color:#FFFFFF;width:20.5%;height:22%;float:right")
#page.img(class_="chart", src_="hist_scaffold.png")
#page.td.close()
#page.div.close()
#page.div.close()
#page.td.close()
#page.tr.close()
page.table.close()
#page.iframe(src_="bar-phylum.png",style_="width:100%;height:100%;hspace=10")
#page.frameset(rows_="100%" ,cols_="100%")
page.td.close()
#page.li("<a target=\"_blank\" href=\"http://cbcb.umd.edu/software/metamos\">metAMOS website</a>")
#page.li("<a href=\"http://cbcb.umd.edu/~mpop/Software.shtml\">Related software</a>")
#page.li("<a href=\"http://cbcb.umd.edu\">CBCB</a>")
# page.li( items[1] )
#page.ul.close( )
#page.div.close()
page.div(id_="content")
#page.div( id_='wrapper')
#page.div( id_="content")
#page.a( "Reference assembly:", class_='internal', href='%s'%(ref_asm) )
#paragraphs = ( ddf )
cnt = 0
#table_html = ""
if 0:
page.table(border="1", style_="width=80%")
for contig in covdata:
if cnt == 0:
#table_html += "<table border=\"1\">\n"
page.tr()
page.td("High Coverage Contig ID")
page.td("Coverage")
page.tr.close()
#table_html += "<tr><td> High Coverage Contig ID </td> <td> Coverage </td></tr>\n"
page.tr()
page.td(contig.split("\t")[0])
page.td(contig.split(" ")[-1])
cnt += 1
'''
#page.table.close()
#page.p( paragraphs )
#page.p(style_="font-size:6px")
page.table(border="0")
#page.tr()
#page.(
if 1:
#table_html = ""
#table_html += "<table border=\"1\">\n"
for contig in rdata:
page.tr()
#table_html += "<tr>\n"
index = 0
for item in contig.split("\t"):
index +=1
if index == 8 or index == 7:
continue
elif index == 1 and "File" not in item:
page.td("<a target=\"_blank\" href=\""+ref_asm+"\">%s</a>"%(ref_asm.split("/")[-1]))
continue
page.td("<p style=\"font-size:15px\">"+item+"</p>")
#table_html += "<td> %s </td> \n"%(item)
page.tr.close()
#table_html += "</tr>\n"
page.table.close()
#table_html += "</table>\n"
#page.p( table_html )
#page.p.close()
page.div.close()
'''
page.td(id_="quick")
page.div(style_="height:100%")
#items = ["<a href=\"http://cbcb.umd.edu/software/metamos\">metAMOS website</a>", ]
#page.ul()
page.br()
page.div(class_="stats")
page.table(class_="stats")
page.add("<tr><td class=\"number\">%s</td><td>Reads</td></tr>" %
intOrZero(readcount))
page.add("<tr><td class=\"number\">%s</td><td>Contigs</td></tr>" %
intOrZero(contigcount))
page.add("<tr><td class=\"number\">%s</td><td>Scaffolds</td></tr>" %
intOrZero(scaffoldcount))
page.add("<tr><td class=\"number\">%s</td><td>ORFs</td></tr>" %
intOrZero(orfcount))
page.add("<tr><td class=\"number\">%s</td><td>Motifs</td></tr>" %
intOrZero(motifcount))
page.table.close()
page.div.close()
page.div.close()
page.td.close()
page.tr.close()
page.table.close()
#page.div( id_="metaphyler", style="float:left;width:28%;height:70%")
#page.img( hspace=10, alt='Abundance', src='bar-phylum.png' )
#page.div.close()
#page.img( hspace=10, width=600, height=500, alt='Abundance', src='bar-phylum.png' )
#page.div.close()
fout = open(html_prefix + "summary.html", 'w')
fout.write(page.__str__())
fout.close()
#!/usr/bin/env python2
#!-*- encoding: cp949 -*-
from pygooglechart import PieChart3D
chart = PieChart3D(250, 100)
chart.add_data([20, 10])
chart.set_pie_labels([u'¾È³ç'.encode('utf-8'), u'¼¼»ó'.encode('utf-8')])
print chart.get_url()
chart.download('pie_ko.png')
def hello_world():
chart = PieChart3D(settings.width, settings.height)
chart.add_data([ord(a) for a in 'hW'])
chart.set_pie_labels(['Hello', 'World'])
chart.download('pie-hello-world.png')
contracts = scraperwiki.sqlite.select('''
contract_info.event_class, SUM(volume)
FROM contract_info INNER JOIN contract_volume
ON contract_info.id = contract_volume.id
WHERE contract_volume.date = ?
GROUP BY event_class
''', latest_date)
volumes = dict([(d['event_class'], d['SUM(volume)']) for d in contracts])
print '<h2>Contract Volume by Category</h2>'
print '<table>'
for k,v in sorted(volumes.items(), key=lambda v:v[1], reverse=True):
print '<tr><td>{}</td><td>{:,}</td></tr>'.format(k,v)
print '</table>'
chart = PieChart3D(300,300)
chart.add_data(volumes.values())
chart.set_pie_labels(volumes.keys())
chart_url = chart.get_url()
print '<img src = "{}">'.format(chart_url)
import scraperwiki
from pygooglechart import PieChart3D
sourcescraper = 'intrade_total_trading_volume'
scraperwiki.sqlite.attach(sourcescraper, 't')
volume = scraperwiki.sqlite.select('* FROM contract_volume')
latest_date = max([v['date'] for v in volume])
if ">phylum" in line:
phylum = True
if len(line) < 3:
continue
data = line.split("\t")
if len(data) < 2:
continue
if not phylum:
continue
ids.append(data[0])
#cov.append(int(float(data[2])))
abund.append(100 * float(data[1]))
# Create a chart object of 200x100 pixels
# chart2 = StackedVerticalBarChart(600, 300)
chart2 = PieChart3D(550, 300)
chart2.set_colours(["0A8C8A", "EBB671", "DE091A"])
# Add some data
chart2.add_data(abund)
# chart2.add_data(abund2)
# Assign the labels to the pie data
chart2.set_pie_labels(ids)
# chart2.set_axis_labels(Axis.BOTTOM, ids)
# Download the chart
try:
chart2.download(prefix + 'abund.png')
except:
print "Warning: could not download abund.png"