Commit b9b28975 authored by Sylvain Jasson's avatar Sylvain Jasson
Browse files

Outputs description

parent 2099e079
...@@ -9,6 +9,8 @@ ...@@ -9,6 +9,8 @@
\usepackage{hyperref} %required by pandoc \usepackage{hyperref} %required by pandoc
\usepackage{svg} \usepackage{svg}
\usepackage{import} %required for svg inkscape import \usepackage{import} %required for svg inkscape import
\usepackage{forest}
\graphicspath{{images/}} \graphicspath{{images/}}
...@@ -26,6 +28,24 @@ breaklines=true ...@@ -26,6 +28,24 @@ breaklines=true
\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}} \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
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\title{Spell-QTL User Manual} \title{Spell-QTL User Manual}
\subtitle{Species perscrutandis enixe locis locabuntur} \subtitle{Species perscrutandis enixe locis locabuntur}
\author{Damien Leroux \and Sylvain Jasson} \author{Damien Leroux \and Sylvain Jasson}
...@@ -316,7 +336,7 @@ Global software organization is displayed in figure \ref{fig:pipeline}. More det ...@@ -316,7 +336,7 @@ Global software organization is displayed in figure \ref{fig:pipeline}. More det
\subsubsection{File format} \subsubsection{File format}
See \texttt{spell-pedigree} man page (at appendix \ref{ch:spell:predigree}) See \texttt{spell-pedigree} man page (at appendix \ref{ch:spell:predigree})
\subsubsection{File sample} \subsubsection{File sample}
\begin{lstlisting}[frame=single,caption={Pedigree (.ped)}] \begin{lstlisting}[frame=single,caption={[Pedigree (.ped input file)]Pedigree (.ped)}]
Founders,1,0,0 Founders,1,0,0
Founders,2,0,0 Founders,2,0,0
Founders,3,0,0 Founders,3,0,0
...@@ -384,7 +404,7 @@ Note that \textbf{CP} and \textbf{ABHCD} formats imply user-made genotype infere ...@@ -384,7 +404,7 @@ Note that \textbf{CP} and \textbf{ABHCD} formats imply user-made genotype infere
Other allele code can be defined via a JSON file. (see in appendix \ref{spell-marker:marker-observation-format-specification} for format and \ref{spell-marker:example-the-02-abhcd-and-cp-formats} for sample files) Other allele code can be defined via a JSON file. (see in appendix \ref{spell-marker:marker-observation-format-specification} for format and \ref{spell-marker:example-the-02-abhcd-and-cp-formats} for sample files)
\subsubsection{File sample} \subsubsection{File sample}
\begin{lstlisting}[frame=single,caption={Marker alleles (.gen)}] \begin{lstlisting}[frame=single,caption={[Marker alleles (.gen input file)]Marker alleles (.gen)}]
data type random example data type random example
42 42 0 0 42 42 0 0
*M1 21221-0212-122-20000-101022220100202102200 *M1 21221-0212-122-20000-101022220100202102200
...@@ -411,7 +431,7 @@ One line per linkage group (space separated) : ...@@ -411,7 +431,7 @@ One line per linkage group (space separated) :
\end{itemize} \end{itemize}
\subsubsection{File sample} \subsubsection{File sample}
\begin{lstlisting}[frame=single,breaklines=false,caption={Genetic map (.map)}] \begin{lstlisting}[frame=single,breaklines=false,caption={[Genetic Map (.map input file)] Genetic map (.map)}]
*Chrom1 3 M11 10.5 M12 30.3 M13 *Chrom1 3 M11 10.5 M12 30.3 M13
*Chrom2 17 M21 5.5 M22 0 M23 2 M24 5 M25 8 M26 11 M27 2.2 M28 2.5 M29 ... *Chrom2 17 M21 5.5 M22 0 M23 2 M24 5 M25 8 M26 11 M27 2.2 M28 2.5 M29 ...
*Chrom3 8 M31 10 M32 10 M33 10 M34 10 M35 10 M36 10 M37 10 M38 *Chrom3 8 M31 10 M32 10 M33 10 M34 10 M35 10 M36 10 M37 10 M38
...@@ -421,7 +441,7 @@ One line per linkage group (space separated) : ...@@ -421,7 +441,7 @@ One line per linkage group (space separated) :
\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 (*) trait name followed by space separated observations (one numerical observation per individual, \texttt{ -} means unobserved).
\subsubsection{File sample} \subsubsection{File sample}
\begin{lstlisting}[frame=single,breaklines=false,caption={Trait observations (.phen)}] \begin{lstlisting}[frame=single,breaklines=false,caption={[Trait observations (.phen input file)]Trait observations (.phen)}]
*trait_1 131.97 113.96 - 125.53 56.31 87.55 73.55 66.6 91.13 5.74 ... *trait_1 131.97 113.96 - 125.53 56.31 87.55 73.55 66.6 91.13 5.74 ...
*trait_2 149.12 -56.72 104.56 100.54 88.49 102.0 65.75 121.94 68.92 ... *trait_2 149.12 -56.72 104.56 100.54 88.49 102.0 65.75 121.94 68.92 ...
*trait_3 147.87 - - 38.53 103.83 95.51 20.05 72.69 66.74 136.95 78.57 ... *trait_3 147.87 - - 38.53 103.83 95.51 20.05 72.69 66.74 136.95 78.57 ...
...@@ -431,6 +451,74 @@ As in MapMaker RAW format, without header : one line per trait beginning with st ...@@ -431,6 +451,74 @@ As in MapMaker RAW format, without header : one line per trait beginning with st
\end{lstlisting} \end{lstlisting}
\chapter{Generated outputs} \chapter{Generated outputs}
\section{General organization}
General output directory organization is :
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[my\_directory
[my\_name.1-point
[...]
]
[my\_name.cache
[my\_name.spell-marker.data]
[my\_name.spell-pedigree.data]
[...]
]
[my\_name.n-point
[...]
]
[my\_name.report
[...]
]
[my\_name.spell-qtl.log
]
]
\end{forest}
\begin{itemize}
\item A common working directory must be set for all 3 executables using command line option \texttt{-wd my\_directory} or \texttt{--work-directory my\_directory}. Every result produced during analysis will be directed to this directory.
\item A configuration name using command line option \texttt{-n my\_name} or \texttt{--name my\_name} is used to name subdirectories.
\item Parental Origin Probabilities are output as CSV files
\begin{description}
\item [1-point] one file per marker,
\item [n-point] one file per linkage group per generation per individual
\end{description}
\item a report containing
\begin{itemize}
\item A text-mode file rendering of the genetic map with the detected QTLs and their confidence interval
\item The model matrix ans the variance-covariance matrix for each selection the detection algorith used
\item The detailed final model including variance-covariance matrix, coefficients, contrasts and contrasts significance
\end{itemize}
\item some hidden files with cached computation results.
\end{itemize}
\begin{appendices} \begin{appendices}
......
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