Extract sequences from a fastx file given a subsequence or identifier
C++ Shell Makefile Python
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fxtract_test
util @ 776ca85
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README.md
fileManager.cpp
fileManager.h
fx.cpp
fx.h
kseq.cpp
kseq.hpp
main.cpp
util.cpp
util.h

README.md

fxtract

Extract sequences from a fastx (fasta or fastq) file given a subsequence. Currently uses a variety of search algorithms depending on the task. Currently searches using a simple substring search for basic tasks but can change to using POSIX regular expressions, PCRE, hash lookups or multi-pattern searching as required. By default will look in the sequence of each record but can be told to look in the header, comment or quality sections of a record.

Installation with pre-compiled binaries

Precompiled binaries are available.

Install from source

The only external dependancy is zlib, PCRE is an optional dependency. Both of these are oftne already installed

To compile, make sure the dependencies above are installed and then hopefully the following will work for you (if not open an issue)

$ git clone --recursive https://github.com/ctSkennerton/fxtract.git
$ cd fxtract
$ make

If PCRE is not installed on your system or if you get an error message during installation try the following

$ make NO_PCRE=1

If you want to check to see if it's installed properly run the tests by

$ make fxtract_test

and see if they pass, I hope that they do.

License

MIT. See LICENSE file for more details