Fast inexact text searching with suffix arrays
Project description
nearmiss
NEARby MISmatch Search
nearmiss is a fast inexact text matching tool for finding repeats of an area around a specific anchor string throughout text, optionally finding matches with substitutions.
It is primarily intended for finding near-match sections of DNA in the vicinity
of specific anchor sequences. The current substitution alphabet is limited to
ACGT
.
The speed of nearmiss comes from a C extension that uses the SA-IS suffix array
library from Yuta Mori and pointer magic instead.
The search time for anchors is O(|anchor| log |text|)
.
The search time for repeats is O(a(sw)^d log t)
, where
a
is the number of anchors founds
is the size of the substitution alphabetw
is the size of the matching windowd
is the maximum desired number of substitutions to allow in the window- and
t
is the size of the search text
Use
>>> from nearmiss import Searcher
>>> seq = "TACTANGGnnnTAAAAGnGG"
>>> searcher = Searcher(seq)
>>> searcher.find_anchors("GG")
[6, 18]
>>> searcher.find_anchors("nGG")
[17]
>>> searcher.find_repeat_counts("GG", (-4, -2), max_distance=1)
{18: [1, 0], 6: [1, 0]}
>>> searcher.find_repeat_counts("GG", (-4, -2), max_distance=2)
{18: [1, 0, 1], 6: [1, 0, 1]}
For more detailed information, see the source documentation with
pydoc nearmiss.Searcher
or help(nearmiss.Searcher)
.
To limit the number of threads used outside the source, set the environment
variable OMP_NUM_THREADS
to the number of desired threads.
Installing
Non-python dependencies
nearmiss uses OpenMP to drastically speed up mismatch searching on many anchors.
To install that on Debian/Ubuntu systems, run sudo apt-get install libomp5
.
with pip
pip install nearmiss
from source
pip install .
in the source directory
Project details
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