This is a light-weight adaptation of parasail and ksw2 to facilitate various types of Smith-Waterman alignment.
More importantly, it facilitates sending an alignment input via standard input and having the output on standard output, with the tool exiting only when standard input is closed.
This allows wrapping this tool in Scala, python, or other programming languages to allow for interactive alignment, without having to restart the tool.
The following four alignment modes are supported:
- Local alignment: a sub-sequence of the query aligned to a sub-sequence of the target (parasail only)
- Glocal: the full query aligned to a sub-sequence of the target (parasail only)
- Extension - a prefix of the query aligned to a prefix of the target (ksw2 only)
- Global - full query aligned to the full target (parasail or ksw2)
Use the -M option to select the alignment mode, and the -l option to select which library (parasail or ksw2) to use.
The utility reads the query and target sequences from standard input, so running it without anything on standard input will cause it to never exit. The query should be on the first line, while the target on the second line. Subsequent lines should alternate between query and target.
This tool can be run interactively. Meaning, the tool reads in one query and target at a time, runs alignment, then writes the alignment output, then waits for more input. Therefore, we can wrap this tool in a process that writes to the standard input of this tool, waits for the alignment result on standard output, then does something else, then feeds more data to standard input. This saves time executing the tool each time for thousands or millions of alignments.
Note: when any of the algorithms open a gap, the gap open plus the gap extension penalty is applied.
Clone this repository:
git clone --recursive git@github.com:nh13/ksw.git
Note the use of --recursive. This is required in order to download all nested git submodules for external repositories.
To get version displayed in the utility, do the following:
cp post-commit .git/hooks/post-commit;
chmod +x .git/hooks/post-commit;
Finally, to compile, type:
make
The executable is named ksw.
To run tests, type:
make test
To install to /usr/local/bin, type:
make install
For a custom location (ex. ~/local/bin), type:
make install PREFIX=~/local/bin
To make a custom tarball, with all sources including sources from submodules, type:
make tarball