Commit 0837fa5b authored by Sylvain Jasson's avatar Sylvain Jasson
Browse files

longer foreword + typos

parent 78823aea
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...@@ -110,7 +110,7 @@ The special text file named \texttt{full\_map.txt} is produced at the root of \t ...@@ -110,7 +110,7 @@ The special text file named \texttt{full\_map.txt} is produced at the root of \t
\begin{figure}[h] \begin{figure}[h]
\includegraphics[width=1.0\textwidth]{full_map.png} \includegraphics[width=1.0\textwidth]{full_map.png}
\caption{screen capture of \texttt{less -RS full\_map.txt} in a \textit{ad hoc} resized terminal. Chromosome names are printed light blue. The chromosome and markers are white. The found QTL and its confidence interval are added in green labeled with trait name (\texttt{t1}), \texttt{@}, QTL position (\texttt{135.34}) and confidence interval (\texttt{[129.246:140.84]})} \caption{screen capture of \texttt{less -RS full\_map.txt} in a \textit{ad hoc} resized terminal. Chromosome names are printed light blue. The chromosome and markers names are white. The found QTL and its confidence interval are added in green labeled with trait name (\texttt{t1}), \texttt{@}, QTL position (\texttt{135.34}) and confidence interval (\texttt{[129.246:140.84]})}
\label{fig:full-map} \label{fig:full-map}
\end{figure} \end{figure}
......
...@@ -8,13 +8,23 @@ ...@@ -8,13 +8,23 @@
\caption{The main Spell-QTL pipeline}\label{fig:pipeline} \caption{The main Spell-QTL pipeline}\label{fig:pipeline}
\end{figure} \end{figure}
Global software organization is displayed in figure \vref{fig:pipeline}. More detailed informations about the main purpose of each part and then about the required input files will be provided in this chapter. Global software organization is displayed in figure \vref{fig:pipeline}.
\section{Minimal session}
A minimal session for Spell-QTL analysis is 3 commands long. For an example to run example 1 from package:
\begin{itemize}
\item \texttt{spell-pedigree -wd my\_directory -n my\_name -p example1.ped}
\item \texttt{spell-marker -wd my\_directory -n my\_name -m F2:A/B example1\_F2.gen -m F2C:A/C example1\_F2C.gen -o F2,F2C}
\item \texttt{spell-qtl -wd my\_directory -n my\_name -P auto -p F2 example1\_F2.phen -p F2C example1\_F2C.phen -gm example1.map}
\end{itemize}
If you want to duplicate these commands, you must check that the input files are available to the programs. You may want to copy them in your test directory, or use an absolute or relative path in you command line.
\section{Software suite details} \section{Software suite details}
\subsection{\texttt{spell-pedigree}} \subsection{\texttt{spell-pedigree}}
\begin{itemize} \begin{itemize}
\item Computes the transition matrices for the Continuous Time Hidden Markov Models (CTHMM). They are the $T_d$ matrices in formula \vref{eq:pop}. The number of hidden states is of course the order od the matrix. \item Computes the transition matrices for the Continuous Time Hidden Markov Models (CTHMM). They are the $T_d$ matrices in formula \vref{eq:pop}. The number of hidden states is of course the order of the matrix.
\item These computations are inherently dependent, so it can only run sequentially. \item These computations are inherently dependent, so it can only run sequentially.
\item Outputs a data file that can be fed to \texttt{spell-marker}. \item Outputs a data file that can be fed to \texttt{spell-marker}.
\end{itemize} \end{itemize}
...@@ -26,7 +36,7 @@ Global software organization is displayed in figure \vref{fig:pipeline}. More de ...@@ -26,7 +36,7 @@ Global software organization is displayed in figure \vref{fig:pipeline}. More de
\item Sequentially, \item Sequentially,
\item Multithreaded, \item Multithreaded,
\item Scheduling jobs on {\em Sun Grid Engine}, \item Scheduling jobs on {\em Sun Grid Engine},
\item Sending jobs to remote machines via \texttt{ ssh} \item Sending jobs to remote machines via \texttt{ssh}
\end{itemize} \end{itemize}
\item Outputs a data file that can be fed to \texttt{spell-qtl}. \item Outputs a data file that can be fed to \texttt{spell-qtl}.
\item Can also output the raw Parental Origin Probabilities. \item Can also output the raw Parental Origin Probabilities.
...@@ -53,7 +63,7 @@ See \texttt{spell-pedigree} man page (at \vref{spell-pedigree:description}.) ...@@ -53,7 +63,7 @@ See \texttt{spell-pedigree} man page (at \vref{spell-pedigree:description}.)
] ]
{input_files/example1.ped} {input_files/example1.ped}
Note that \begin{itemize} Note that: \begin{itemize}
\item the first line is expected to be header only and will be ignored by \texttt{spell-pedigree}. \item the first line is expected to be header only and will be ignored by \texttt{spell-pedigree}.
\item Only four columns are used, any additional column will be silently ignored by \texttt{spell-pedigree} \item Only four columns are used, any additional column will be silently ignored by \texttt{spell-pedigree}
\end{itemize} \end{itemize}
...@@ -62,11 +72,11 @@ Note that \begin{itemize} ...@@ -62,11 +72,11 @@ Note that \begin{itemize}
\subsection{Marker observations} \subsection{Marker observations}
\subsubsection{File format} \subsubsection{File format}
\texttt{spell-marker} understand a few common formats, based on MapMaker RAW format (without traits) : \texttt{spell-marker} understand a few common formats, based on MapMaker RAW format (without traits):
\begin{itemize} \begin{itemize}
\item A line beginning with \texttt{data type} followed by ignored text (\textit{e.g.} line 1 in sample \vref{file:gen}) \item A line beginning with \texttt{data type} followed by ignored text (\textit{e.g.} line 1 in sample \vref{file:gen})
\item A line containing four integer values : number of individuals, number of markers, two ignored values (\textit{e.g.} line 2 in sample \vref{file:gen}) \item A line containing four integer values: number of individuals, number of markers, two ignored values (\textit{e.g.} line 2 in sample \vref{file:gen})
\item A line per marker beginning with starred(*) marker name followed by a space and by allele observed or inferred for each individual (a character per individual). (\textit{e.g.} line 3-39 in sample \vref{file:gen}) \item A line per marker beginning with starred(\texttt{*}) marker name followed by a space and by allele observed or inferred for each individual (a character per individual). (\textit{e.g.} line 3-39 in sample \vref{file:gen})
\end{itemize} \end{itemize}
Build in allele code are : Build in allele code are :
...@@ -82,7 +92,7 @@ Build in allele code are : ...@@ -82,7 +92,7 @@ Build in allele code are :
\item The child in not typed. The possible genotypes are $A|A$, $A|B$, $B|A$ and $B|B$. This is encoded by the character \texttt{ -} in MapMaker. \item The child in not typed. The possible genotypes are $A|A$, $A|B$, $B|A$ and $B|B$. This is encoded by the character \texttt{ -} in MapMaker.
\end{itemize} \end{itemize}
The parental origin letters can be overridden in the command line. The parental origin letters can be overridden in the command line.
\item[CP] Outbred observations as defined in Cathagene. These observations are relevant for all known phases situations, including cases where one parent is homozygous, when 3 or 4 different alleles are present. Lets consider the cross $A|B \times C|D$: The possibles child genotypes are $A|C$, $A|D$, $B|C$ and $B|D$. Carthagene format actually enables the user to express any subset of the 4 different possibilities using a single hexadecimal digit (0-f). \item[CP] Outbred observations as defined in Cathagene. These observations are relevant for all known phase situations, including cases where one parent is homozygous, when 3 or 4 different alleles are present. Lets consider the cross $A|B \times C|D$: The possibles child genotypes are $A|C$, $A|D$, $B|C$ and $B|D$. Carthagene format actually enables the user to express any subset of the 4 different possibilities using a single hexadecimal digit (0-f).
\begin{center} \begin{center}
\begin{tabular}{cc} \begin{tabular}{cc}
...@@ -123,7 +133,7 @@ Other allele code can be defined via a JSON file. (see in appendix \vref{spell-m ...@@ -123,7 +133,7 @@ Other allele code can be defined via a JSON file. (see in appendix \vref{spell-m
Note that \begin{itemize} Note that \begin{itemize}
\item in line 1 \texttt{F2} after \texttt{ data type} is irrelevant for \texttt{spell-marker}. \item in line 1 \texttt{F2} after \texttt{ data type} is irrelevant for \texttt{spell-marker}.
\item in line 2 \texttt{0 0} after \texttt{100 37} is irrelevant \texttt{spell-marker}. \item in line 2 \texttt{0 0} after \texttt{100 37} is irrelevant for \texttt{spell-marker}.
\end{itemize} \end{itemize}
...@@ -131,7 +141,7 @@ Note that \begin{itemize} ...@@ -131,7 +141,7 @@ Note that \begin{itemize}
\subsubsection{File format} \subsubsection{File format}
One line per linkage group (space separated) : One line per linkage group (space separated) :
\begin{itemize} \begin{itemize}
\item Starred(*) name for this linkage group \item Starred(\texttt{*}) name for this linkage group
\item Number of markers in the linkage group \item Number of markers in the linkage group
\item Name of first marker \item Name of first marker
\item Series of distance in cM and name of next marker \item Series of distance in cM and name of next marker
...@@ -147,7 +157,7 @@ One line per linkage group (space separated) : ...@@ -147,7 +157,7 @@ One line per linkage group (space separated) :
\subsection{Trait observations} \subsection{Trait observations}
\subsubsection{File format} \subsubsection{File format}
As in MapMaker RAW format, without header : one line per trait beginning with starred (*) trait name followed by space separated observations (one numerical observation per individual, \texttt{ -} means unobserved). As in MapMaker RAW format, without header : one line per trait beginning with starred(\texttt{*}) trait name followed by space separated observations (one numerical observation per individual, \texttt{ -} means unobserved).
\subsubsection{File sample} \subsubsection{File sample}
\lstinputlisting[numbers=left,frame=single,breaklines=false,caption={[Trait observations (.phen input file)]Trait observations (example1\_F2.phen from three\_parents\_F2 example)}]{input_files/example1_F2.phen} \lstinputlisting[numbers=left,frame=single,breaklines=false,caption={[Trait observations (.phen input file)]Trait observations (example1\_F2.phen from three\_parents\_F2 example)}]{input_files/example1_F2.phen}
......
...@@ -13,7 +13,7 @@ ...@@ -13,7 +13,7 @@
\usepackage{forest} \usepackage{forest}
\usepackage{inconsolata} % alternative typewriter font \usepackage{inconsolata} % alternative typewriter font
\usepackage{hyperref} \usepackage{hyperref}
\usepackage[T1]{fontenc} %ensures copy paste work with underscores !
\graphicspath{{images/}} \graphicspath{{images/}}
...@@ -49,7 +49,7 @@ basicstyle=\ttfamily ...@@ -49,7 +49,7 @@ basicstyle=\ttfamily
% %
\subject{\includegraphics[width=0.25\textwidth]{images/logotype-INRA-RVB.jpg}}
\title{Spell-QTL User Manual} \title{Spell-QTL User Manual}
\subtitle{Species perscrutandis enixe locis locabuntur} \subtitle{Species perscrutandis enixe locis locabuntur}
...@@ -58,7 +58,8 @@ basicstyle=\ttfamily ...@@ -58,7 +58,8 @@ basicstyle=\ttfamily
\input{version.tex} \input{version.tex}
} }
\publishers{\includegraphics[width=0.3\textwidth]{images/logo_MIAT.png}} \publishers{\includegraphics[width=0.35\textwidth]{images/logo_MIAT.png}
}
...@@ -73,15 +74,23 @@ basicstyle=\ttfamily ...@@ -73,15 +74,23 @@ basicstyle=\ttfamily
\chapter*{Foreword} \chapter*{Foreword}
Spell-QTL\footnote{ {\em Species perscrutandis enixe locis locabutur} means {\em The characters will be localized using an zealous loci inspection}, the very purpose of the software} \paragraph{} Spell-QTL
is a software suite allowing to detect QTLs in any crossing design. is a software suite allowing to detect QTLs in any crossing design. Spell acronym is for {\em Species Perscrutandis Enixe Locis Locabutur}. This means {\em The characters will be localized using an zealous loci inspection}, the very purpose of the software. If you read this manual, you already know what QTL stands for.
We - Damien Leroux and Sylvain Jasson - are developping Spell-QTL at MIAT, a research lab from INRA French National Institute for Agricultural Research. We are located near Toulouse, in the French Occitanie region.
\paragraph{} When the project started, we were just planning to rewrite our legacy code MCQTL, using modern C++. After decades of development and many contributors - most of them not even reachable - MCQTL had reached the stage of "Hydra code": every bug correction, every improvement was made at very high cost.
As the project was moving forward, and as we were thinking it would be a quick and easy release, we discover that some hypothesis that were made in MCQTL, were no mode valid with dealing with modern crosses (MAGIC, AIC...)
This work switched from engineering project to research project inadvertently, and we are very happy about that !
It is developed at MIAT lab by Damien Leroux and Sylvain Jasson. It is available at \url{https://mulcyber.toulouse.inra.fr/frs/?group_id=204} under Gnu Public License. \paragraph{} Both the software and this manual are work under progress: feed-back is welcome and appreciated.
\vspace*{\fill} \vspace*{\fill}
\noindent Spell-QTL is available at \url{https://mulcyber.toulouse.inra.fr/frs/?group_id=204} under Gnu Public License. \noindent Spell-QTL is available at \url{https://mulcyber.toulouse.inra.fr/frs/?group_id=204} under Gnu Public License.
\begin{center} \begin{center}
\includegraphics[clip, trim=0.5cm 8cm 0.5cm 14cm,width=0.25\columnwidth]{pdfs/gpl-v3-logo} \includegraphics[clip, trim=0.5cm 7.9cm 0.5cm 14cm,width=0.25\columnwidth]{pdfs/gpl-v3-logo}
\end{center} \end{center}
This manual is licensed under a \href{https://creativecommons.org/licenses/by-sa/4.0/}{Creative Commons Attribution-ShareAlike 4.0 International License}. This manual is licensed under a \href{https://creativecommons.org/licenses/by-sa/4.0/}{Creative Commons Attribution-ShareAlike 4.0 International License}.
\begin{center} \begin{center}
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