brentp / biostuff (http://hackmap.blogspot.com/)

miscellaneous bioinformatics modules.

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commit 62: 5e09d0e13822
parent 61: eb9ab1710e6e
child 63: 6d084649fe4e
bump version. update changelog for 0.3.7 default0.3.7
brentp
3 months ago

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nwalign  
pyfasta  
simpletable  
skidmarks  
.hgignore 55 B 5 months ago fix errors in setup.py and dont use sudo in upload.sh
.hgtags 141 B 3 months ago Added tag 0.3.6 for changeset 52238ee2288b
README.rst 2.2 KB 5 months ago update readme

README

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')])