README.md

What's this?

This is a sub project of altorf, analyzing altorf from genome perspective. It creates simulated genomes for each species and compares altorf properties with real genome. Programs are organized into further sub-directories depending on the stage of analysis. Basically written in C++ or Python3, and also Shell Scripts are used to create pipelines.

Workflow

Follow this flow from top to bottom. For further information, please refer to README on each sub directories.

speciespick

• Chooses which species in RefSeq to analyze.

preprocess

• Splits downloaded .fna files and fills ambiguous bases randomly if needed.

genomeshuffle

• Creates simulated genomes according to .fna & .gff files.

patternanalyze

• Analyze pattern of altorf comparing real genome and simulated genome.

Prerequisites

I chose SeqAn as C++ library in order to process DNA sequence efficiently and to make biological fileI/0 easier.

• seqan: https://www.seqan.de/

  • An open source C++ library of efficient algorithms and data structures for the analysis of sequences.
  • For installation, please refered to http://seqan.readthedocs.io/en/master/Infrastructure/Use/Install.html
    0. Mac: brew install homebrew/science/seqan 0. servers: clone github repository https://github.com/seqan/seqan

• CMake: https://cmake.org/

  • seqan recommends compilation with CMake http://seqan.readthedocs.io/en/master/Infrastructure/Use/FindSeqAnCMake.html

• Anaconda (ver 3.X)

• BioPython

Compilation of .cpp

• Commands below creates binary file in build directory.

cd $PATH_TO_DESIGNATED_DIR
mkdir build
cd build
cmake ../src
make

• In case you obtained SeqAn from a git clone, you need to specify the install location and include path.
  • cmake ../src -DCMAKE_PREFIX_PATH="$HOME/software/seqan/util/cmake" -DSEQAN_INCLUDE_PATH="$HOME/software/seqan/include"
    • Please change paths according to your environment.