Commit 9b9cdefb authored by Sylvain Jasson's avatar Sylvain Jasson
Browse files

use examples from package

parent b9b28975
user_manual.pdf : spell-pedigree.tex spell-marker.tex spell-qtl.tex spell-qtl-examples.tex version.tex user_manual.tex images/Spell-pipeline2.svg
EXAMPLE_DIR = ~/INSTALL_DIR/SPELL_TEST/spell_qtl-0.1-alpha.1-Linux/share/spell-qtl/examples/three_parents_F2
user_manual.pdf : spell-pedigree.tex spell-marker.tex spell-qtl.tex spell-qtl-examples.tex version.tex user_manual.tex images/Spell-pipeline2.svg inputs
pdflatex --shell-escape user_manual.tex && pdflatex --shell-escape user_manual.tex
version.tex :
......@@ -20,11 +21,21 @@ 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
inputs :
mkdir -p input_files
awk -v len=73 '{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }' $(EXAMPLE_DIR)/example1.map > input_files/example1.map
awk -v len=73 '{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }' $(EXAMPLE_DIR)/example1_F2.phen > input_files/example1_F2.phen
awk -v len=73 '{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }' $(EXAMPLE_DIR)/example1_F2.gen > input_files/example1_F2.gen
awk -v len=73 '{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }' $(EXAMPLE_DIR)/example1.ped > input_files/example1.ped
clean:
rm -f *.aux *.log *.pdf *.toc *.out *.lol
rm -f version.tex
rm -f spell-pedigree.tex spell-marker.tex spell-qtl.tex spell-qtl-examples.tex
rm -f images/*.pdf images/*.pdf_tex
rm -rf input_files
veryclean: clean
rm -f *~
......@@ -336,19 +336,13 @@ Global software organization is displayed in figure \ref{fig:pipeline}. More det
\subsubsection{File format}
See \texttt{spell-pedigree} man page (at appendix \ref{ch:spell:predigree})
\subsubsection{File sample}
\begin{lstlisting}[frame=single,caption={[Pedigree (.ped input file)]Pedigree (.ped)}]
Founders,1,0,0
Founders,2,0,0
Founders,3,0,0
Founders,4,0,0
F1,5,1,2
F1,6,3,4
CP,7,5,6
F2,8,7,7
F3,9,8,8
F3,10,8,8
F3,11,8,8
\end{lstlisting}
\lstinputlisting[numbers=left,
frame=single,
breaklines=false,
caption={[Pedigree (.ped input file)]Pedigree (selected lines from example1.ped from three\_parents\_F2 example)},
linerange={1-12,107-112}
]
{input_files/example1.ped}
\subsection{Marker observations}
......@@ -404,21 +398,15 @@ 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)
\subsubsection{File sample}
\begin{lstlisting}[frame=single,caption={[Marker alleles (.gen input file)]Marker alleles (.gen)}]
data type random example
42 42 0 0
*M1 21221-0212-122-20000-101022220100202102200
*M2 012120-0221010220101112222101211122120211-
*M3 0221022000211200012112-020000-101221222202
*M4 00112-021012200110101221221222112120100120
*M5 2211-00211121002221--2-20002102-1011220211
*M6 01211-201202221121002-12211200000001011001
*M7 202212202-00--10-101221200-112001-110-220-
*M8 222-22-02102002002220112-021-022--12012-11
*M9 0210-10-1122212-21000-2200-121200200222211
...
\end{lstlisting}
Note that \texttt{ data type} is irrelevant
\lstinputlisting[numbers=left,
frame=single,
breaklines=false,
caption={[Marker alleles (.gen input file)]Marker alleles (example1\_F2.gen from three\_parents\_F2 example)},
%linerange={1-8,35-39}
]
{input_files/example1_F2.gen}
Note that line 1 \texttt{F2} after \texttt{ data type} is irrelevant
\subsection{Genetic map}
\subsubsection{File format}
......@@ -431,24 +419,14 @@ One line per linkage group (space separated) :
\end{itemize}
\subsubsection{File sample}
\begin{lstlisting}[frame=single,breaklines=false,caption={[Genetic Map (.map input file)] Genetic map (.map)}]
*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 ...
*Chrom3 8 M31 10 M32 10 M33 10 M34 10 M35 10 M36 10 M37 10 M38
\end{lstlisting}
\lstinputlisting[numbers=left,frame=single,breaklines=false,caption={[Genetic Map (.map input file)] Genetic map (example1.map from three\_parents\_F2 example)}]{input_files/example1.map}
\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, \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}
\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_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_4 57.52 143.51 128.02 41.53 122.34 100.11 123.41 74.11 119.22 ...
*trait_5 125.69 197.13 - 152.77 74.41 188.16 64.8 108.04 89.6 154.62 ...
...
\end{lstlisting}
\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}
\chapter{Generated outputs}
\section{General organization}
......
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