In [46]:

    

from pytadbit.parsers.hic_parser import load_hic_data_from_reads
from cPickle import load


    

In [19]:

    

%matplotlib inline


    

In [3]:

    

reso = 300000
base_path = 'results/both/03_filtering/valid_reads12.tsv'
bias_path = 'results/both/04_normalizing/biases_{0}.pick'
bads_path = 'results/both/04_normalizing/bad_columns_{0}.pick'


    

In [6]:

    

def my_load_hic_data(reso):
    hic_data = load_hic_data_from_reads(base_path, resolution=reso)
    hic_data.bias = load(open(bias_path.format(reso)))
    hic_data.bads = load(open(bads_path.format(reso)))
    return hic_data


    

In [8]:

    

hic_data = my_load_hic_data(reso)


    

In [9]:

    

! mkdir -p results/fragment/both/05_segmenting


    

In [31]:

    

crm = 'chr18'
corr = hic_data.find_compartments(
        show=True, crms=[crm], vmin=-0.2, vmax=0.2, label_compartments='none',
        savedata='results/fragment/both/05_segmenting/compartments_{0}_{1}.tsv'.format(crm, reso))


    

    













    




---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/home/student/.miniconda2/lib/python2.7/site-packages/IPython/core/formatters.pyc in __call__(self, obj)
    305                 pass
    306             else:
--> 307                 return printer(obj)
    308             # Finally look for special method names
    309             method = get_real_method(obj, self.print_method)

/home/student/.miniconda2/lib/python2.7/site-packages/IPython/core/pylabtools.pyc in <lambda>(fig)
    238 
    239     if 'png' in formats:
--> 240         png_formatter.for_type(Figure, lambda fig: print_figure(fig, 'png', **kwargs))
    241     if 'retina' in formats or 'png2x' in formats:
    242         png_formatter.for_type(Figure, lambda fig: retina_figure(fig, **kwargs))

/home/student/.miniconda2/lib/python2.7/site-packages/IPython/core/pylabtools.pyc in print_figure(fig, fmt, bbox_inches, **kwargs)
    122 
    123     bytes_io = BytesIO()
--> 124     fig.canvas.print_figure(bytes_io, **kw)
    125     data = bytes_io.getvalue()
    126     if fmt == 'svg':

/home/student/.miniconda2/lib/python2.7/site-packages/matplotlib/backend_bases.pyc in print_figure(self, filename, dpi, facecolor, edgecolor, orientation, format, **kwargs)
   2196                 bbox_artists = kwargs.pop("bbox_extra_artists", None)
   2197                 if bbox_artists is None:
-> 2198                     bbox_artists = self.figure.get_default_bbox_extra_artists()
   2199 
   2200                 bbox_filtered = []

/home/student/.miniconda2/lib/python2.7/site-packages/matplotlib/figure.pyc in get_default_bbox_extra_artists(self)
   1690                 bbox_artists.extend(ax.get_default_bbox_extra_artists())
   1691         # we don't want the figure's patch to influence the bbox calculation
-> 1692         bbox_artists.remove(self.patch)
   1693         return bbox_artists
   1694 

ValueError: list.remove(x): x not in list





    






<matplotlib.figure.Figure at 0x7f5b09e04f10>

In [32]:

    

! head -n 20 results/fragment/both/05_segmenting/compartments_chr2_300000.tsv


    

    




## CHR chr2	Eigenvector: 1
#start	end	density	type
chr2	0	2	0.08	
chr2	3	4	0.03	
chr2	5	5	0.01	
chr2	6	8	0.07	
chr2	9	12	0.14	
chr2	13	22	1.03	
chr2	23	23	0.01	
chr2	24	27	0.12	
chr2	28	38	0.90	
chr2	39	39	0.01	
chr2	40	41	0.03	
chr2	42	50	0.64	
chr2	51	51	0.01	
chr2	52	54	0.07	
chr2	55	55	0.01	
chr2	56	65	0.72	
chr2	66	68	0.08	
chr2	69	77	0.68	

In [35]:

    

from pytadbit import Chromosome


    

In [37]:

    

crm = Chromosome('18')
crm.add_experiment('HindIII', 
                   hic_data='results/HindIII/04_normalizing/100000_raw/chr18.mat', 
                   norm_data='results/HindIII/04_normalizing/100000_norm/chr18.mat',
                   resolution=100000)
crm.add_experiment('MboI', 
                   hic_data='results/MboI/04_normalizing/100000_raw/chr18.mat',
                   norm_data='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 [38]:

    

crm.visualize([('HindIII', 'MboI')])


    

In [39]:

    

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


    

In [41]:

    

crm.find_tad(['HindIII', 'MboI'], n_cpus=8)


    

In [42]:

    

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


    

In [43]:

    

crm.visualize([('HindIII', 'MboI')], normalized=True, paint_tads=True, focus=(670, 770))


    

In [44]:

    

crm.experiments


    

    
Out[44]:





[Experiment HindIII (resolution: 100 kb, TADs: 57, Hi-C rows: 804, normalized: visibility),
 Experiment MboI (resolution: 100 kb, TADs: 62, Hi-C rows: 804, normalized: visibility)]

In [47]:

    

ali = crm.align_experiments()


    

In [48]:

    

ali.draw()


    

In [45]:

    

crm.save_chromosome('results/crm18.tdb')