Operations on VariantCallSupport objects

In [1]:

    

import sys, os
from bl.vl.kb import KnowledgeBase

OME_HOST = os.getenv('OME_HOST', 'localhost')
OME_USER = os.getenv('OME_USER', 'test')
OME_PASSWD = os.getenv('OME_PASSWD', 'test')
CHECK_OME_VERSION = os.getenv('CHECK_OME_VERSION', "True") == "True"

BaseProxy = KnowledgeBase(driver='omero')

class Proxy(BaseProxy):
  def get_objects_dict(self, klass):
    return dict((o.label, o) for o in super(Proxy, self).get_objects(klass))

kb = Proxy(OME_HOST, OME_USER, OME_PASSWD, check_ome_version=CHECK_OME_VERSION)

def cleanup():
  print "# disconnecting the kb"
  kb.disconnect()

sys.exitfunc = cleanup

print
print "### KB ENV PRELOADED ###"
print "# connected to %s" % OME_HOST
print "# knowledge base: kb"
print "# extra method: kb.get_objects_dict"
print "########################"


    

    




### KB ENV PRELOADED ###
# connected to biobank04.crs4.it
# knowledge base: kb
# extra method: kb.get_objects_dict
########################

In [2]:

    

vcss = kb.get_objects_dict(kb.VariantCallSupport)


    

In [3]:

    

vcss


    

    
Out[3]:





{'human_exom-V1-test+GRCh37.1': <bl.vl.kb.drivers.omero.variant_call_support.VariantCallSupport at 0x4845090>}

In [4]:

    

vcs = kb.genomics.get_vcs_by_label('human_exom-V1-test+GRCh37.1')


    

In [5]:

    

ref_gen = vcs.referenceGenome


    

In [6]:

    

ref_gen.label


    

    
Out[6]:





'GRCh37.1'

In [7]:

    

ref_gen.nChroms


    

    
Out[7]:





26

In [8]:

    

nodes = vcs.get_nodes()
for i in range(1, ref_gen.nChroms):
    print 'Chrom {} -> {} snps'.format(i, sum(nodes['chrom'] == i))


    

    




Chrom 1 -> 25100 snps
Chrom 2 -> 17502 snps
Chrom 3 -> 14762 snps
Chrom 4 -> 10377 snps
Chrom 5 -> 11518 snps
Chrom 6 -> 15466 snps
Chrom 7 -> 11323 snps
Chrom 8 -> 9069 snps
Chrom 9 -> 10365 snps
Chrom 10 -> 9641 snps
Chrom 11 -> 15840 snps
Chrom 12 -> 12472 snps
Chrom 13 -> 4441 snps
Chrom 14 -> 7831 snps
Chrom 15 -> 8355 snps
Chrom 16 -> 10551 snps
Chrom 17 -> 13235 snps
Chrom 18 -> 3797 snps
Chrom 19 -> 15212 snps
Chrom 20 -> 6517 snps
Chrom 21 -> 2866 snps
Chrom 22 -> 5225 snps
Chrom 23 -> 5205 snps
Chrom 24 -> 141 snps
Chrom 25 -> 226 snps

In [9]:

    

vcs.get_nodes()[0:10]


    

    
Out[9]:





array([(1, 762320), (1, 861349), (1, 865545), (1, 865584), (1, 865625),
       (1, 865628), (1, 865662), (1, 865665), (1, 865694), (1, 865700)], 
      dtype=[('chrom', '<i8'), ('pos', '<i8')])

In [10]:

    

vcs2 = vcs.selection(((1, 762320), (1, 865625)))


    

In [11]:

    

vcs3 = vcs.selection(((1, 865545), (1, 865665)))


    

In [12]:

    

vcs4 = vcs2.intersection(vcs3)


    

In [13]:

    

vcs4.get_nodes()


    

    
Out[13]:





array([(1, 865545), (1, 865584)], 
      dtype=[('chrom', '<i8'), ('pos', '<i8')])

In [14]:

    

vcs5 = vcs2.union(vcs3)


    

In [15]:

    

vcs5.get_nodes()


    

    
Out[15]:





array([(1, 762320), (1, 861349), (1, 865545), (1, 865584), (1, 865625),
       (1, 865628), (1, 865662)], 
      dtype=[('chrom', '<i8'), ('pos', '<i8')])

In [16]:

    

vcs6 = vcs2.complement(vcs3)


    

In [17]:

    

vcs6.get_nodes()


    

    
Out[17]:





array([(1, 762320), (1, 861349)], 
      dtype=[('chrom', '<i8'), ('pos', '<i8')])

In [18]:

    

len(vcs6)


    

    
Out[18]:





2

In [19]:

    

vcs6.label


    

    
Out[19]:





'0e88cf825c854cfcaaddf4d57dad80e2'

In [20]:

    

kb.get_objects_dict(kb.VariantCallSupport)


    

    
Out[20]:





{'human_exom-V1-test+GRCh37.1': <bl.vl.kb.drivers.omero.variant_call_support.VariantCallSupport at 0x4845090>}

In [21]:

    

vcs6.save()


    

In [22]:

    

kb.get_objects_dict(kb.VariantCallSupport)


    

    
Out[22]:





{'0e88cf825c854cfcaaddf4d57dad80e2': <bl.vl.kb.drivers.omero.variant_call_support.VariantCallSupport at 0x4870e50>,
 'human_exom-V1-test+GRCh37.1': <bl.vl.kb.drivers.omero.variant_call_support.VariantCallSupport at 0x4845090>}

In [23]:

    

kb.delete(vcs6)


    

In [24]:

    

kb.get_objects_dict(kb.VariantCallSupport)


    

    
Out[24]:





{'human_exom-V1-test+GRCh37.1': <bl.vl.kb.drivers.omero.variant_call_support.VariantCallSupport at 0x4845090>}

In [25]:

    

vcs6.get_nodes()


    

    
Out[25]:





array([(1, 762320), (1, 861349)], 
      dtype=[('chrom', '<i8'), ('pos', '<i8')])

In [ ]: