jperelshteyn / matchseq

CLI tool for searching for nucleotide sequence in DNA stream

matchseq

Memory-safe nucleotide subsequence search tool. It will search a stream of nucleotides and print every occurrence of a specified subsequence with optional left and right context.

Install

git clone https://github.com/jperelshteyn/matchseq.git
cd matchseq
python setup.py install

Command Line Arguments

• -T target subsequence (required)
• -x length of left context (optional)
• -y length of right context (optional)

Requirements

Input nucleotide sequence as well as the target subsequence must only consist of base values: A, C, G, T The end of sequence character is ε - nothing will be searched after it.

Usage

echo "ACACGTCAε" | matchseq -T:ACGT -x:1 -y:2
...
C ACGT CA