def _linksToDownloads(sample, assembler):
div_id = "collapseDownload" + sample.name()
with h.div(class_="accordion-group"):
with h.div(class_="accordion-heading"):
h.a("Downloads", href="#"+div_id, class_="accordion-toggle",
data_toggle="collapse")
with h.div(class_="accordion-body collapse in", id=div_id):
with h.div(class_="accordion-inner"):
with h.div(class_="row-fluid", id="downloadPane"):
with h.div(class_="row-fluid"):
with h.div(class_="span12"):
h.p("Download all your assembly result files.")
with h.div(style="padding-top:5px"):
with h.p():
index = 0
downloads = sample.downloads(assembler)
for descr, url in downloads.items():
rurl = os.path.relpath(url, DIRNAME)
index += 1
if index % 5 != 1:
h.UNESCAPED((" |"
" "))
h.UNESCAPED("<a target='_blank' "
"href='%s'>"
"<i class='icon-download'>"
"</i>%s</a>" % (rurl, descr))
if index % 5 == 0:
h.br()
def _linksToDownloads(sample, assembler):
div_id = "collapseDownload" + sample.name()
with h.div(class_="accordion-group"):
with h.div(class_="accordion-heading"):
h.a("Downloads",
href="#" + div_id,
class_="accordion-toggle",
data_toggle="collapse")
with h.div(class_="accordion-body collapse in", id=div_id):
with h.div(class_="accordion-inner"):
with h.div(class_="row-fluid", id="downloadPane"):
with h.div(class_="row-fluid"):
with h.div(class_="span12"):
h.p("Download all your assembly result files.")
with h.div(style="padding-top:5px"):
with h.p():
index = 0
downloads = sample.downloads(assembler)
for descr, url in downloads.items():
rurl = os.path.relpath(url, DIRNAME)
index += 1
if index % 5 != 1:
h.UNESCAPED((" |"
" "))
h.UNESCAPED("<a target='_blank' "
"href='%s'>"
"<i class='icon-download'>"
"</i>%s</a>" %
(rurl, descr))
if index % 5 == 0:
h.br()
def _assemblyStats(sample, assembler):
def _assemblySettingsTable():
with h.table(class_="table table-condensed"):
h.tr(h.th("Parameter"), h.th("Value"))
for param, value in sample.assemblySettings(assembler).items():
h.tr(h.td(param), h.td(value))
def _assemblyMetricsTable(kind):
with h.table(class_="table table-condensed"):
with h.tr():
h.th("Metric")
with h.th():
h.UNESCAPED("Large " + kind + "s (≥ 500bp)")
h.th("All " + kind + 's')
for metric, value in sample.metrics(assembler, kind).items():
if len(value) == 1:
h.tr(h.td(metric), h.td(value[0], colspan='2'))
else:
h.tr(h.td(metric), h.td(value[0]), h.td(value[1]))
div_id = "collapseStats" + sample.name()
with h.div(class_="accordion-group"):
with h.div(class_="accordion-heading"):
h.a("Assembly Statistics",
href="#" + div_id,
class_="accordion-toggle",
data_toggle="collapse")
with h.div(id=div_id, class_="accordion-body collapse in"):
with h.div(class_="accordion-inner"):
with h.div(class_="row-fluid", id="statPane"):
with h.div(class_="row-fluid"):
with h.div(class_="span12"):
if sample.name() != '.':
h.p("Assembly summary statistics for ",
sample.name() + ".")
with h.div(style="padding-top:5px"):
_assemblySettingsTable()
with h.div(style="padding-top:10px"):
_assemblyMetricsTable("Contig")
if sample.hasScaffolds(assembler):
with h.div(style="padding-top:10px"):
_assemblyMetricsTable("Scaffold")
def _assemblyStats(sample, assembler):
def _assemblySettingsTable():
with h.table(class_="table table-condensed"):
h.tr(h.th("Parameter"), h.th("Value"))
for param, value in sample.assemblySettings(assembler).items():
h.tr(h.td(param), h.td(value))
def _assemblyMetricsTable(kind):
with h.table(class_="table table-condensed"):
with h.tr():
h.th("Metric")
with h.th():
h.UNESCAPED("Large " + kind + "s (≥ 500bp)")
h.th("All " + kind + 's')
for metric, value in sample.metrics(assembler, kind).items():
if len(value) == 1:
h.tr(h.td(metric), h.td(value[0], colspan='2'))
else:
h.tr(h.td(metric), h.td(value[0]), h.td(value[1]))
div_id = "collapseStats" + sample.name()
with h.div(class_="accordion-group"):
with h.div(class_="accordion-heading"):
h.a("Assembly Statistics", href="#"+div_id,
class_="accordion-toggle", data_toggle="collapse")
with h.div(id=div_id, class_="accordion-body collapse in"):
with h.div(class_="accordion-inner"):
with h.div(class_="row-fluid", id="statPane"):
with h.div(class_="row-fluid"):
with h.div(class_="span12"):
if sample.name() != '.':
h.p("Assembly summary statistics for ",
sample.name() + ".")
with h.div(style="padding-top:5px"):
_assemblySettingsTable()
with h.div(style="padding-top:10px"):
_assemblyMetricsTable("Contig")
if sample.hasScaffolds(assembler):
with h.div(style="padding-top:10px"):
_assemblyMetricsTable("Scaffold")
# creating nice HTML reports with summaries about multiple samples
import hypertext as h
from ordereddict import OrderedDict # TorrentServer VM has only python 2.6 :(
import locale # for printing numbers with thousands delimited by commas
import json
import os
import sys
# FIXME: hardcoded version
sys.path.append(os.path.join(os.environ['DIRNAME'], "bin", "quast-2.3"))
from libs.N50 import N50
from libs.fastaparser import get_lengths_from_fastafile, read_fasta
MIRA_LINK = str(h.a("MIRA", target="_blank",
href="http://mira-assembler.sourceforge.net"))
SPADES_LINK = str(h.a("SPAdes", target="_blank",
href="http://bioinf.spbau.ru/spades"))
ASSEMBLER_LINKS = { 'mira' : MIRA_LINK,
'spades' : SPADES_LINK }
DIRNAME = os.environ['TSP_FILEPATH_PLUGIN_DIR']
def _alertAboutAssemblerWebsite(assembler):
link = ASSEMBLER_LINKS[assembler]
with h.div(id="alertUser", class_="row-fluid"):
with h.div(class_="span12"):
with h.div(class_="alert alert-info"):
h.button("x", class_="close", data_dismiss="alert",
# creating nice HTML reports with summaries about multiple samples
import hypertext as h
from ordereddict import OrderedDict # TorrentServer VM has only python 2.6 :(
import locale # for printing numbers with thousands delimited by commas
import json
import os
import sys
# FIXME: hardcoded version
sys.path.append(os.path.join(os.environ['DIRNAME'], "bin", "quast-2.3"))
from libs.N50 import N50
from libs.fastaparser import get_lengths_from_fastafile, read_fasta
MIRA_LINK = str(
h.a("MIRA", target="_blank", href="http://mira-assembler.sourceforge.net"))
SPADES_LINK = str(
h.a("SPAdes", target="_blank", href="http://bioinf.spbau.ru/spades"))
ASSEMBLER_LINKS = {'mira': MIRA_LINK, 'spades': SPADES_LINK}
DIRNAME = os.environ['TSP_FILEPATH_PLUGIN_DIR']
def _alertAboutAssemblerWebsite(assembler):
link = ASSEMBLER_LINKS[assembler]
with h.div(id="alertUser", class_="row-fluid"):
with h.div(class_="span12"):
with h.div(class_="alert alert-info"):
h.button("x",