Source

biostuff /

Filename Size Date modified Message
nwalign
pyfasta
simpletable
skidmarks
55 B
323 B
2.2 KB

biostuff

Skidmarks

find runs (non-randomness) in sequences

>>> from skidmarks import gap_test, wald_wolfowitz, auto_correlation, serial_test
>>> serial_test('110000000000000111111111111')
{'chi': 18.615384615384617, 'p': 0.00032831021826061683}

nwalign

fast Needleman-Wunsch global alignment in cython. command-line and python usage

>>> import nwalign as nw
>>> nw.global_align("CEELECANTH", "PELICAN", matrix='PAM250')
('CEELECANTH', '-PELICA--N')

pyfasta

pythonic access to fasta sequence files

>>> from pyfasta import Fasta
>>> f = Fasta('some.fasta')
>>> f.keys()
['chr1', 'chr2', 'chr3']

>>> f['chr1'][10:20]
'actgatcgga'

simpletable

pytables wrapper for easy access to s structured data.

>>> class ATable(SimpleTable):
...     x = tables.Float32Col()
...     y = tables.Float32Col()
...     name = tables.StringCol(16)


>>> tbl = ATable('test_docs.h5', 'atable1')

# insert as with pytables.
>>> row = tbl.row
>>> for i in range(50):
...    row['x'], row['y'] = i, i * 10
...    row['name'] = "name_%i" % i
...    row.append()
>>> tbl.flush()

#access the entire array via the numpy array interface
>>> import numpy as np
>>> np.asarray(tbl)



#query the data (query() alias of tables' readWhere()
>>> tbl.query('(x > 4) & (y < 70)') #doctest: +NORMALIZE_WHITESPACE
array([('name_5', 5.0, 50.0), ('name_6', 6.0, 60.0)],
    dtype=[('name', '|S16'), ('x', '<f4'), ('y', '<f4')])
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