Commit efbdaa95 authored by Carsten Kemena's avatar Carsten Kemena

adding first manual

parent 370d5e57
Subproject commit eb77e85ca54c9c06fbc50f004667404e5fd0a763
Subproject commit 5ef51990748613d3da50c048967f9a4a50677e83
\documentclass[a4paper,10pt]{scrreprt}
\usepackage[utf8]{inputenc}
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\usepackage[hidelinks]{hyperref}
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{ %
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title=\lstname % show the filename of files included with \lstinputlisting; also try caption instead of title
}
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% Title Page
\title{RADIANT 0.9-beta\\User Manual}
\author{Carsten Kemena\\c.kemena@uni-muenster.de}
\begin{document}
\maketitle
\chapter{Installation}
\section{Download}
There are two ways to download RADIANT. Either you can download it using git or manually from the website. Both ways are described below.
If you use git you can easily update to a newer version when available.
\subsection{Download using git}
Use git to clone the repository and download BioSeqDataLib as a submodule:
\begin{lstlisting}[style=MyBashStyle]
git clone https://ebbgit.uni-muenster.de/domainWorld/RADIANTIANT.git
cd RADIANT
git submodule init
git submodule update
\end{lstlisting}
\subsection{Manual Download}
You can download the compressed source code from our gitlab web-page \url{https://ebbgit.uni-muenster.de/domainWorld/RADIANT}. Additionally you will have to download the BioSeqDataLib from \url{https://ebbgit.uni-muenster.de/domainWorld/BioSeqDataLib} and uncompress it in the libs directory of RADIANT.
\subsection{Compilation \& Installation}
Inside the source folder a build directory is needed in which the code will be compiled. CMake is used to find all the needed requirements of the library.
\begin{lstlisting}[style=MyBashStyle]
mkdir build
cd build
cmake ..
make
\end{lstlisting}
\subsection{Updating}
Sometimes it will be necessary to update RADIANT either because it contains some new features or because we unfortunately had a bug somewhere that we have now fixed. If you used \texttt{git} for the original download you can simply use \texttt{git} to update your code. Simply change into the RADIANT directory and type:
\begin{lstlisting}[style=MyBashStyle]
git pull
git submodule foreach git pull origin master
\end{lstlisting}
You now simply follow again the steps in the Installation section. If you downloaded the code without git you will have to download the latest version and replace the old one with it. Do not forget to update the \texttt{BioSeqDataLib} folder as well.
\chapter{Annotating domains}
RADIANT needs two input arguments. One is the proteome or transcriptome to annotate, the second is the database to use. For the database only the prefix needs to be given.
\begin{lstlisting}[style=MyBashStyle]
radiant -i proteome.fa -d <path to database>/pfam31 -o annotation.txt
\end{lstlisting}
\subsection{Output}
The output of RADIANT is designed to be similar to the PfamScan output but contains less columns. Lines starting with a
\#’ are comments and contain information about the program and format version and as well about the query and database files used.
\begin{verbatim}
# RADIANT 1.0.0
# RADIANT output format: 1.0
# run at Wed Aug 2 16:24:46 2017
#
# Options used:
#-----------------------------------------------------------------------------
# query file: <path>/Homo_sapiens.GRCh38.pep.all.fa.iso.fa
# database file: <path>/pfam31
# translate: false
#-----------------------------------------------------------------------------
#
# <seq id> <match start> <match end> <hmm acc> <hmm name> <type> <clan>
ENSP00000362111.4 27 27 PF00335 Tetraspannin Family CL0347
ENSP00000362122.4 120 120 PF04089 BRICHOS Domain No_clan
ENSP00000360640.4 36 36 PF00535 Glycos_transf_2 Family CL0110
ENSP00000356744.1 42 42 PF00069 Pkinase Domain CL0016
ENSP00000352276.4 184 184 PF14868 DUF4487 Family No_clan
ENSP00000363117.3 91 91 PF00018 SH3_1 Domain CL0010
ENSP00000363117.3 152 152 PF00017 SH2 Domain CL0541
ENSP00000363117.3 272 272 PF07714 Pkinase_Tyr Domain CL0016
\end{verbatim}
\section{Advantages \& Disadvantages}
Advantages:
\begin{itemize}
\item very fast
\item can be used to get a good overview over existing domains
\item well interfaced with DOGMA
\end{itemize}
RADIANT has currently the following restrictions:
\begin{itemize}
\item short domains and domains that are similar to other domains will likely not be detected
\item high RAM consumption ($\approx$ 7GB)
\end{itemize}
Some of these shortcomings will be solved in the future versions. Others are intrinsically to the approach used will persist.
\chapter{Construction database}
\end{document}
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