miscellaneous tools for molecular biology.

** Requirements

Python 3.3
Cython
numpy

** Commands

seqview: render overview image of sequence, primers, bisulfite sequence results.
get_genbank: get GenBank file from ncbi.
geneview: render overview image of gene sequence, annotation
seqdb: seqtool database manager. see database/README

sequencing: align ab1 sequencing result file to reference sequence

bisearch: design primer based on primer3 algorithm.
virtualpcr: PCR primer alignment tool using bowtie

primers: calculate primers properties
primer: calculate primer properties
probe: calculate TaqMan probe properties
bisulfite: show bisulfite converted sequence
rpm: calculate rpm of centrifuge machine
abiview: .ab1 viewer

** configfile location

for Mac OS X

configfile: '/Users/_____/Library/Application Support/seqtool/config.cfg'
cache dir:  '/Users/_____/Library/Caches/seqtool'



see appdirs documentation for other platforms.

** bootstrap

% virtualenv --version
1.10.1
% python3.3 --version
Python 3.3.2

% virtualenv --python=python3.3 --no-site-packages env
% source env/bin/activate
% pip install numpy
% pip install Cython
% python setup.py develop

** databases

see database/README

** building boost
no user-config.bjam required.

% cd boost_1_52_0
% ./boostrap.sh --with-toolset=clang
% ./b2 toolset=clang cxxflags="-std=c++11 -stdlib=libc++" linkflags="-stdlib=libc++" install
% clang++ -Wall -std=c++0x -stdlib=libc++ -L/usr/local/lib -I/usr/local/include -O1 -lboost_program_options c/bisearch.cpp c/main.cpp -o bin/bisearch

You must link boost_program_options

** TODO

- general
    - better logging
    
- seqview
    - zoom button in seqv
    - web server implementation
    - pcr virtualpcr integration

- new
    - plasmid fragment analysis and view
    - local database. MySQL, emsemble.

- bisearch
    - MSP
    - python interface