Commit dcb304da authored by Sylvain Jasson's avatar Sylvain Jasson
Browse files

adding output files samples

parent 9b9cdefb
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
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 outputs
pdflatex --shell-escape user_manual.tex && pdflatex --shell-escape user_manual.tex
version.tex :
......@@ -30,12 +31,19 @@ inputs :
awk -v len=73 '{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }' $(EXAMPLE_DIR)/example1.ped > input_files/example1.ped
outputs :
spell-pedigree -wd my_directory -n my_name -p $(EXAMPLE_DIR)/example1.ped
spell-marker -wd my_directory -n my_name -m F2:A/B $(EXAMPLE_DIR)/example1_F2.gen -m F2C:A/C $(EXAMPLE_DIR)/example1_F2C.gen -o F2,F2C -O1
#spell-qtl -wd my_directory -n my_name -p F2 $(EXAMPLE_DIR)/example1_F2.phen -p F2C $(EXAMPLE_DIR)/example1_F2C.phen -gm $(EXAMPLE_DIR)/example1.map -P auto QTL-detection CIM connected
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 *~
rm -rf input_files
rm -rf my_directory
......@@ -484,18 +484,33 @@ General output directory organization is :
\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 [1-point] one file per marker (with pedigree like structure),
\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 model matrix ans the variance-covariance matrix for each selection the detection algorithm 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}
\section{Output files samples}
\subsection{1-point POP}
%\lstinputlisting[%numbers=left,
%frame=single,
%breaklines=false,
%caption={[1-point output file] 1-point output file (selected lines from my\_name.pedigree-and-probabilities.M_1_1.csv from my\_directory/my\_name.1-point/)},
%linerange={1-12,107-112}
% ]
\lstinputlisting[numbers=left,
frame=single,
caption={[1-point output file] 1-point output file (selected lines from file \texttt{my\_name.pedigree-and-probabilities.M\_1\_1.csv} in directory \texttt{my\_directory/my\_name.1-point/} ) },%(selected lines from my\_name.pedigree-and-probabilities.M_1_1.csv from my\_directory/my\_name.1-point/)},
linerange={1-12,107-112}
]{my_directory/my_name.1-point/my_name.pedigree-and-probabilities.M_1_1.csv}
Note that you must use \texttt{-01} command line option in \texttt{spell-marker} in order to generate these files.
\begin{appendices}
......
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