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 found
• s is the size of the substitution alphabet
• w is the size of the matching window
• d 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