Alignment class

class pytadbit.alignment.Alignment(name, alignment, experiments, score=None)

draw(focus=None, extras=None, savefig=None)

Draw alignments as a plot.

Parameters:

• focus (None) – can pass a tuple (bin_start, bin_stop) to display the alignment between these genomic bins
• extras (None) – list of coordinates (genomic bin) where to draw a red cross

get_column(cond1, cond2=None, min_num=None)

Get a list of column responding to a given characteristic.

Parameters:

• cond1 – can be either a column number or a function to search for a given condition that may fulfill boundaries.
• cond2 (None) – a second function to search for a given condition that may fulfill boundaries.
• min_num (None) – Number of boundaries in a given column that have to pass the defined conditions (all boundaries may pass them by default).

Returns:

a list of column, each column represented by a tuple which first element is the column number in the alignment and second element is the list of boundaries in this column.

Example

ali = Alignment('ALL', crm.get_alignment('ALL'),
                crm.experiments, score)
ali.get_column(3)
# [(3, [>55<, ,>56<, >55<, >58<])]

# now we want boundaries with high scores
cond1 = lambda x: x['score'] > 5
# and we want boundaries to be detected in Experiments exp1 and exp2
cond2=lambda x: x['exp'] in ['exp1', 'exp2']

ali.get_column(cond1=cond1, cond2=cond2, min_num=2)
# [(33, [>268<, >192<, >-<, >-<]),     
#  (46, [>324<, >323<, >335<, >329<]), 
#  (51, [>348<, >335<, >357<, >347<]), 
#  (56, [>374<, >358<, >383<, >-<]),   
#  (64, [>397<, >396<, >407<, >-<]),   
#  (77, [>444<, >442<, >456<, >-<])]   

itercolumns()

Iterate over columns in the alignment

iteritems()

Iterate over experiment names and aligned boundaries

itervalues()

Iterate over experiment names and aligned boundaries

write_alignment(names=None, xpers=None, string=False, title='', ftype='ansi')

Print alignment of TAD boundaries between different experiments.

Alignment are displayed with colors according to the tadbit confidence score for each boundary.

Parameters:

• names (None) – if None print all experiments
• xpers (None) – if None print all experiments
• string (False) – return string instead of printing
• ftype (ansi) – display colors in ‘ansi’ or ‘html’ format

class pytadbit.alignment.TAD(thing, i, exp)

Specific class of TADs, used only within Alignment objects. It is directly inheriting from python dict. a TAD these keys:

• ‘start’: position of the TAD
• ‘end’: position of the TAD
• ‘score’: of the prediction of boundary
• ‘brk’: same as ‘end’
• ‘pos’: in the alignment (column number)
• ‘exp’: Experiment this TAD belongs to
• ‘index’: of this TAD within all TADs in the Experiment

pytadbit.alignment.randomization_test(xpers, score=None, num=1000, verbose=False, max_dist=100000, rnd_method='interpolate', r_size=None, method='reciprocal')

Return the probability that original alignment is better than an alignment of randomized boundaries.

Parameters:

• tads – original TADs of each experiment to align
• distr – the function to interpolate TAD lengths from probability
• score (None) – just to print it when verbose
• num (1000) – number of random alignment to generate for comparison
• verbose (False) – to print something nice
• method (interpolate) – how to generate random tads (alternative is ‘shuffle’). ‘interpolate’ will calculate the distribution of TAD lengths, and generate a random set of TADs according to this distribution (see pytadbit.alignment.generate_rnd_tads()). In contrast, the ‘shuffle’ method uses directly the set of observed TADs and shuffle them (see pytadbit.alignment.generate_shuffle_tads()).

pytadbit.alignment.generate_rnd_tads(chromosome_len, distr, start=0)

Generates random TADs over a chromosome of a given size according to a given distribution of lengths of TADs.

Parameters:

• chromosome_len – length of the chromosome
• distr – function that returns a TAD length depending on a p value
• bin_size – size of the bin of the Hi-C experiment
• start (0) – starting position in the chromosome

Returns:

list of TADs

pytadbit.alignment.generate_shuffle_tads(tads)

Returns a shuffle version of a given list of TADs

Parameters:tads – list of TADs Returns:list of shuffled TADs