In [1]:
# run this cell first to set up appropriate objects
import os
token = os.environ["KB_AUTH_TOKEN"]
# these are for client-server communication
from doekbase.data_api.annotation.genome_annotation.api import GenomeAnnotationClientAPI
from doekbase.data_api.taxonomy.taxon.api import TaxonClientAPI
from doekbase.data_api.sequence.assembly.api import AssemblyClientAPI
# the ObjectClientAPI is not ready yet, coming soon
taxonurl='https://ci.kbase.us/services/data/taxon'
assemblyurl='https://ci.kbase.us/services/data/assembly'
genomeannotationurl='https://ci.kbase.us/services/data/genome_annotation'
# hard-coded workspace reference for now, an arabidopsis genome
ref='2844/12'
ref="ReferenceEnsemblPlantGenomeAnnotations/3847_EnsembleRelease30"
In [67]:
annoapi = GenomeAnnotationClientAPI(genomeannotationurl, token, ref)
print "new annotation client"
assemblyref = annoapi.get_assembly()
print "assembly "+assemblyref
assemblyapi = AssemblyClientAPI(assemblyurl, token, assemblyref)
contigs = assemblyapi.get_contig_ids()
contig_lens = assemblyapi.get_contig_lengths()
contig_lens_vals = contig_lens.values()
#print contig_lengths.values()
new annotation client
assembly 4435/72/2
In [68]:
from plotly import __version__
from plotly.offline import download_plotlyjs, init_notebook_mode, iplot
print __version__ # requires version >= 1.9.0
init_notebook_mode()
1.9.5
In [69]:
iplot([{"x": [1, 2, 3], "y": [3, 1, 6]}])
In [70]:
from plotly.graph_objs import *
import numpy as np
#minx = min(contig_lengths_vals)
#maxx = max(contig_lengths_vals)
minx =1000000000
maxx=0
for elm in contig_lens_vals:
if elm < minx:
minx = elm
if elm > maxx:
maxx = elm
print str(minx) +"\t"+ str(maxx)
binsize = 1000
bins = (maxx - minx)/binsize
xbins = np.linspace(min,max,binsize)#xbins=bins,
iplot([Histogram(x=contig_lens_vals, autobinx='true')])#, xbins=[20]#,xbins=xbins
1003 62308140
In [65]:
?Histogram
In [23]:
<histogram-object>.help('xbins')
File "<ipython-input-23-b2a3fbe29570>", line 1
<histogram-object>.help('xbins')
^
SyntaxError: invalid syntax
In [55]:
xbins
Out[55]:
array([ 1.00300000e+03, 6.33725065e+04, 1.25742013e+05,
1.88111520e+05, 2.50481026e+05, 3.12850533e+05,
3.75220039e+05, 4.37589546e+05, 4.99959052e+05,
5.62328559e+05, 6.24698065e+05, 6.87067572e+05,
7.49437078e+05, 8.11806585e+05, 8.74176091e+05,
9.36545598e+05, 9.98915104e+05, 1.06128461e+06,
1.12365412e+06, 1.18602362e+06, 1.24839313e+06,
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6.21210315e+07, 6.21834010e+07, 6.22457705e+07,
6.23081400e+07])
In [ ]:
Content source: kbase/data_api
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