def station_metadata(stations):
network_file = get_resource('asos_networks')
station_mapping = pd.read_csv(network_file)
network_query = (station_mapping.iem_network.str.contains('ASOS')) | (
station_mapping.iem_network == 'AWOS')
query = (station_mapping.stid.isin(stations)) & network_query
return station_mapping[query]
def build_info_panel(self, data):
html_win = ClickableHtmlWindow(self.lst, size=(-1, 180))
html_win.attach_to_frame(self, 0)
#style=wx.html.HW_SCROLLBAR_NEVER)
html_text = u"<table><tr>"
img_file = os.path.join(config.images_folder, data['filename'] + '.jpg')
if os.path.exists(img_file):
html_text += u'<td width="100" rowspan="2">\
<img src="{0}"></td>\n'.format(img_file)
else:
html_text += u'<td width="100" rowspan="2"></td>'
# imdb icon
html_text += u'<td><a href="http://imdb.com/title/{0}">\
<img src="{1}"></a></td></tr>'.format(data['imdbID'],
config.get_resource('images', 'imdb-logo.png'))
print html_text
# details
html_text += u"<tr><td>" + self.generate_label_text(data) + u"</td></tr>"
html_text += u"</table>"
html_win.SetPage(html_text)
return html_win
def __init__(self, input, output, *args, **kwargs):
self.init('macse')
self.version_jar()
self.check_input('-i', input)
self.args += ('-o', output)
self.args += args
mem = 0.9 * utils.mem_to_mb(config.get_resource('memory'))
self.run_jar('%dM' % mem)
def __init__(self, input, *args, **kwargs):
self.init('insert_stats', **kwargs)
self.version('-v')
self.check_input('-i', input)
self.args += ('-m', kwargs.get('max_insert',
config.get_resource('max_insert_size')))
self.args += args
self.run()
def create_policy(self):
rule_declarations = config.get_resource('authz')
policy = authz.Policy(error_factory=errors.AuthzError, aspect='server')
for decl in rule_declarations:
policy.declare(decl)
policy.context.update({'s': self})
return policy
def add_openmp(self):
"""
Indicates that this wrapper should use OpenMP by setting the
$OMP_NUM_THREADS environment variable equal to the number of threads
specified in the BioLite configuration file.
"""
threads = min(int(config.get_resource('threads')), self.max_concurrency)
self.env['OMP_NUM_THREADS'] = str(threads)
def generate(self, path):
path = self.path + path
bower_versions = config.bower_versions()
decls = config.get_resource('js_manifest')
decls = config.deep_interpolate(decls, bower_versions)
for decl in decls:
if 'min-href' in decl and decl['min-href'] == path:
return 'text/javascript', self.minify_js(decl)
decls = config.get_resource('css_manifest')
decls = config.deep_interpolate(decls, bower_versions)
for decl in decls:
if 'min-href' in decl and decl['min-href'] == path:
return 'text/css', self.minify_css(decl)
raise tornado.web.HTTPError(400,
"No matching minification declaration.")
def __init__(self, input, iworm, *args, **kwargs):
self.init('chrysalis', **kwargs)
self.add_threading('-cpu')
self.add_openmp()
self.check_input('-i', input)
self.check_input('-iworm', iworm)
mem = utils.mem_to_mb(config.get_resource('memory'))
self.args += ('-sort_buffer_size', '%dM' % int(0.8 * mem))
self.args += args
self.run()
def add_threading(self, flag):
"""
Indicates that this wrapper should use threading by appending an
argument with the specified `flag` followed by the number of threads
specified in the BioLite configuration file.
"""
threads = min(int(config.get_resource('threads')), self.max_concurrency)
if threads > 1:
self.args.append(flag)
self.args.append(threads)
def __init__(self, commands, *args, **kwargs):
self.init('parallel', **kwargs)
self.version('--version')
self.args += (
'--gnu', '-a', commands, '-j',
kwargs.get('threads', config.get_resource('threads')))
hostlist = config.get_resource_default('hostlist', None)
if hostlist:
self.args += ('-S', hostlist)
if self.cwd:
self.args += ('--wd', self.cwd)
else:
self.args += ('--wd', os.getcwd())
self.args += args
self.run()
def __init__(self, inputs, *args, **kwargs):
self.init("spades.py", **kwargs)
self.name = "spades"
self.version()
self.add_threading("-t")
mem = 0.9 * utils.mem_to_mb(config.get_resource('memory')) / 1024
self.args += ("-m", max(1, int(mem)))
# Detect inputs
if isinstance(inputs, basestring):
self.check_input('-s', inputs)
elif len(inputs) == 1:
self.check_input('-s', inputs[0])
elif len(inputs) == 2:
self.check_input('-1', inputs[0])
self.check_input('-2', inputs[1])
else:
utils.die("expected either 1 (SE) or 2 (PE) inputs")
self.args += args
self.run()
def __init__(self, input, kmer, *args, **kwargs):
self.init('jellyfish', **kwargs)
self.version('--version')
#
# From the Jellyfish manual (section 2.3), hash size in bytes is:
#
# 2^l * (2k-l+r+1)/8
#
# s = 2^l is the hash size parameter given by -s. By default, r=5 and
# letting l be 0:
#
# s ~= 8 * mem / (2k + 6)
#
mem = 1048576 * utils.mem_to_mb(config.get_resource('memory'))
mem = 2 ** int(math.log(8 * mem / (2*kmer + 6) , 2))
self.args += ('count', '-m', kmer, '-s', mem)
self.add_threading('-t')
self.check_input(None, input)
self.args += args
self.run()
def __init__(self, inputs, *args, **kwargs):
self.init('trinity', **kwargs)
self.version('--version')
# Detect inputs
if isinstance(inputs, basestring):
self.check_input('--single', inputs)
elif len(inputs) == 1:
self.check_input('--single', inputs[0])
elif len(inputs) == 2:
self.check_input('--left', inputs[0])
self.check_input('--right', inputs[1])
else:
utils.die("expected either 1 (SE) or 2 (PE) inputs")
# Detect file type
ext = os.path.splitext(self.args[-1])[1]
if ext == '.fa':
self.args += ('--seqType', 'fa')
elif ext == '.fq':
self.args += ('--seqType', 'fq')
else:
utils.info("warning: could not determine sequence type of inputs")
# Java uses roughly 2 CPUs per Butterfly call with GC etc. so reduce
# the number of threads by half.
#threads = kwargs.get('threads', int(config.get_resource('threads')))
#self.max_concurrency = max(1, threads/2)
mem = utils.mem_to_mb(config.get_resource('memory'))
self.args += ("--JM", "%dG" % max(1, int(0.8*mem/1024)))
max_insert = kwargs.get(
'max_insert',
diagnostics.lookup_insert_size().max)
if max_insert:
self.args += ('--group_pairs_distance', int(max_insert))
self.add_threading('--CPU')
self.args += args
self.run()
def __init__(self, **kwargs):
self.init('oma', **kwargs)
parameters = """
ReuseCachedResults := true;
NP := %d;
MinScore := 181;
LengthTol := 0.61;
StablePairTol := 1.81;
VerifiedPairTol := 1.53;
MinSeqLen := 50;
StableIdsForGroups := false;
DoHierarchicalGroups := true;
MaxTimePerLevel := 1200;
SpeciesTree := 'estimate';
ReachabilityCutoff := 0.65;
UseEsprit := false;
DistConfLevel := 2;
MinProbContig := 0.4;
MaxContigOverlap := 5;
MinSeqLenContig := 20;
MinBestScore := 250;
""" % int(config.get_resource('threads'))
open(os.path.join(self.cwd, 'parameters.drw'), 'w').write(parameters)
self.run()
def find_class(name):
cls = get_resource(name)
if not cls:
raise ConfigurationException('Could not find APIResource class %r' % name)
return cls
def set_icon(self):
ib = wx.IconBundle()
ib.AddIconFromFile(config.get_resource('images', 'MDB_all.ico'),
wx.BITMAP_TYPE_ICO)
self.SetIcons(ib)
def authz_declarations(self):
decls = config.get_resource('authz')
return json_encode(decls)
def stylesheets(self):
bower_versions = config.bower_versions()
decls = config.get_resource('css_manifest')
decls = config.deep_interpolate(decls, bower_versions)
return self.prepare_resources(decls)