Identifying TADs

In [1]:

    

from pytadbit import Chromosome


    

In [2]:

    

crm = Chromosome('chr18')


    

In [11]:

    

'/media/storage/Notebooks2/fransua/results/MboI/'
'/04_normalizing/100000_raw/chr18.mat'

'/media/storage/Notebooks2/fransua/results/HindIII/'
'/04_normalizing/100000_norm/chr18.mat'


    

    
Out[11]:





'/04_normalizing/100000_norm/chr18.mat'

In [4]:

    

crm.add_experiment('MboI', 
                   hic_data='/media/storage/Notebooks2/fransua/results/MboI/04_normalizing/1000000_raw/chr18.mat', 
                   norm_data='/media/storage/Notebooks2/fransua/results/MboI/04_normalizing/100000_norm/chr18.mat',
                   resolution=100000)


    

    




/home/student/.miniconda2/lib/python2.7/site-packages/pytadbit/parsers/hic_parser.py:247: UserWarning: WARNING: matrix not symmetric: summing cell_ij with cell_ji
  warn('WARNING: matrix not symmetric: summing cell_ij with cell_ji')

In [5]:

    

print crm


    

    




Chromosome chr18:
   1  experiments loaded: MboI
   0  alignment loaded: 
   species         : UNKNOWN
   assembly version: UNKNOWN

In [12]:

    

crm.add_experiment('HindIII', 
                   hic_data='/media/storage/Notebooks2/fransua/results/HindIII/04_normalizing/1000000_raw/chr18.mat', 
                   norm_data='/media/storage/Notebooks2/fransua/results/HindIII/04_normalizing/100000_norm/chr18.mat',
                   resolution=100000)


    

In [13]:

    

print crm


    

    




Chromosome chr18:
   2  experiments loaded: MboI, HindIII
   0  alignment loaded: 
   species         : UNKNOWN
   assembly version: UNKNOWN

In [33]:

    

crm.find_tad(['HindIII','MboI'],n_cpus=20)


    

In [34]:

    

crm.tads()


    

    




---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-34-e45d4f08c79d> in <module>()
----> 1 crm.tads()

AttributeError: 'Chromosome' object has no attribute 'tads'

In [22]:

    

crm.visualize([('HindIII', 'MboI')],normalized=True,paint_tads=True)


    

In [27]:

    

crm.find_tad(['HindIII', 'MboI'], n_cpus=10)


    

In [28]:

    

crm.visualize([('HindIII', 'MboI')], normalized=True, paint_tads=True, )


    

In [23]:

    

ali = crm.align_experiments(randomize=True, rnd_num=100)


    

In [24]:

    

ali, pvals = ali


    

In [25]:

    

pvals


    

    
Out[25]:





(0.32499999999999996, 0.0, 0.5384615384615384, 0.5714285714285714)

In [26]:

    

ali.draw()


    

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