Commit 1b76b172 authored by Sylvain Jasson's avatar Sylvain Jasson
Browse files

Cleaner doc duid

parent d8be4b42
......@@ -6,15 +6,19 @@ version.tex :
spell-pedigree.tex : ../man/spell-pedigree.1.md
/usr/bin/pandoc ../man/spell-pedigree.1.md --listings -f markdown -t latex -o spell-pedigree.tex
sed -i s/\\label\{/\label\{spell-pedigree:/g spell-pedigree.tex
spell-marker.tex : ../man/spell-marker.1.md
/usr/bin/pandoc ../man/spell-marker.1.md --listings -f markdown -t latex -o spell-marker.tex
sed -i s/\\label\{/\label\{spell-marker:/g spell-marker.tex
spell-qtl.tex : ../man/spell-qtl.1.md
/usr/bin/pandoc ../man/spell-qtl.1.md --listings -f markdown -t latex -o spell-qtl.tex
sed -i s/\\label\{/\label\{spell-qtl:/g spell-qtl.tex
spell-qtl-examples.tex : ../man/spell-qtl-examples.1.md
/usr/bin/pandoc ../man/spell-qtl-examples.1.md --listings -f markdown -t latex -o spell-qtl-examples.tex
sed -i s/\\label\{/\label\{spell-qtl-examples:/g spell-qtl-examples.tex
clean:
rm -f *.aux *.log *.pdf *.toc *.out *.lol
......
\documentclass[openright,oneside,10pt,DIV=11]{scrreprt}
\documentclass[oneside,10pt,DIV=11]{scrreprt}
\usepackage[toc,page]{appendix}
\usepackage{url}
\usepackage{listings}
......@@ -286,7 +286,7 @@ Global software organization is displayed in figure \ref{fig:pipeline}. More det
\section{Software suite details}
\subsection{\texttt{spell-pedigree}}
\begin{itemize}
\item Computes the transition matrices for the Continuous Time Hidden Markov Models (The $T_d$ matrices in formula \ref{eq:pop}).
\item Computes the transition matrices for the Continuous Time Hidden Markov Models (CTHMM). They are the $T_d$ matrices in formula \ref{eq:pop}.
\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}.
\end{itemize}
......@@ -298,7 +298,7 @@ Global software organization is displayed in figure \ref{fig:pipeline}. More det
\item Sequentially,
\item Multithreaded,
\item Scheduling jobs on {\em Sun Grid Engine},
\item Sending jobs to remote machines via {\tt ssh}
\item Sending jobs to remote machines via \texttt{ ssh}
\end{itemize}
\item Outputs a data file that can be fed to \texttt{spell-qtl}.
\item Can also output the raw Parental Origin Probabilities.
......@@ -336,22 +336,22 @@ F3,11,8,8
\subsubsection{File format}
\texttt{spell-marker} understand a few common formats, based on MapMaker RAW format (without traits) :
\begin{itemize}
\item A line beginning with {\tt data type} followed by ignored text
\item A line beginning with \texttt{ data type} followed by ignored text
\item A line containing four integer values : number of markers, number of individuals, two ignored values
\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).
\end{itemize}
Build in allele code are :
\begin{description}
\item[02] SNP observations, where 0 and 2 are homozygous and 1 is heterozygous. These observations type are relevant for any individual in the pedigree.
\item[02] SNP observations, where 0 and 2 are homozygous and 1 is heterozygous. These observations type are relevant for any individual in the pedigree, including parents. \texttt{spell-marker} will then perform inference of possible genotypes and inference of possible states in the CTHMM.
\item[ABHCD] MapMaker like Parental Origin inferred observations. These are relevant for inbred lines crosses products. Let's consider the cross $A|A \times B|B$:
\begin{itemize}
\item The child is typed A and the allele A is not dominant. The only possible genotype is $A|A$. This is encoded by the character {\tt A} in MapMaker.
\item The child is typed A and the allele A is dominant. The possible genotype are $A|A$, $A|B$ and $B|A$. This is encoded by the character {\tt D} in MapMaker.
\item The child is typed B and the allele B is not dominant. The only possible genotype is $B|B$. This is encoded by the character {\tt B} in MapMaker.
\item The child is typed B and the allele B is dominant. The possible genotype are $A|B$, $B|A$ and $B|B$. This is encoded by the character {\tt C} in MapMaker.
\item The child is typed AB (the allele A and B are codominant). The possible genotype are $A|B$ and $B|A$. This is encoded by the character {\tt H} 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 {\tt -} in MapMaker.
\item The child is typed A and the allele A is not dominant. The only possible genotype is $A|A$. This is encoded by the character \texttt{ A} in MapMaker.
\item The child is typed A and the allele A is dominant. The possible genotype are $A|A$, $A|B$ and $B|A$. This is encoded by the character \texttt{ D} in MapMaker.
\item The child is typed B and the allele B is not dominant. The only possible genotype is $B|B$. This is encoded by the character \texttt{ B} in MapMaker.
\item The child is typed B and the allele B is dominant. The possible genotype are $A|B$, $B|A$ and $B|B$. This is encoded by the character \texttt{ C} in MapMaker.
\item The child is typed AB (the allele A and B are codominant). The possible genotype are $A|B$ and $B|A$. This is encoded by the character \texttt{ H} 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}
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).
......@@ -379,7 +379,9 @@ e & $A|D$,$B|C$,$B|D$ \\
\end{center}
\end{description}
Other allele code can be defined via a JSON file. (see appendix \ref{ch:spell:marker} for format and sample files)
Note that \textbf{CP} and \textbf{ABHCD} formats imply user-made genotype inference. Depending on generation, \texttt{spell-marker} will perform further genotype inference and HMM state inference using pedigree.
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}
\begin{lstlisting}[frame=single,caption={Marker alleles (.gen)}]
......@@ -396,7 +398,7 @@ data type random example
*M9 0210-10-1122212-21000-2200-121200200222211
...
\end{lstlisting}
Note that {\tt data type} is irrelevant
Note that \texttt{ data type} is irrelevant
\subsection{Genetic map}
\subsubsection{File format}
......@@ -417,7 +419,7 @@ One line per linkage group (space separated) :
\subsection{Trait observations}
\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, {\tt -} 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}
\begin{lstlisting}[frame=single,breaklines=false,caption={Trait observations (.phen)}]
*trait_1 131.97 113.96 - 125.53 56.31 87.55 73.55 66.6 91.13 5.74 ...
......@@ -437,11 +439,17 @@ As in MapMaker RAW format, without header : one line per trait beginning with st
\input{spell-pedigree.tex}
\fussy
\chapter{\texttt{spell-marker} man page} \label{ch:spell:marker}
\sloppy
\input{spell-marker.tex}
\fussy
\chapter{\texttt{spell-qtl} man page}
\sloppy
\input{spell-qtl.tex}
\fussy
\chapter{spell-qtl-examples man page}
\sloppy
\input{spell-qtl-examples.tex}
\fussy
\end{appendices}
\lstlistoflistings
......
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