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.

LaGuer/genome