Changeset 15827

Timestamp:

05/03/12 23:04:53 (13 months ago)

Author:

coissac

Message:

patch the installer for easy_install and pip

Location:

trunk

Files:

• .pydevproject (modified) (1 diff)
• .settings/org.eclipse.core.resources.prefs (modified) (1 diff)
• MANIFEST.in (modified) (1 diff)
• README (added)
• doc/sphinx/source/optionsSet/sequenceFilter.txt (modified) (1 diff)
• doc/theorie/LCS-SIMD/Matrix.xlsx (modified) (previous)
• doc/theorie/Quality-Score/Quality-Score.aux (modified) (1 diff)
• doc/theorie/Quality-Score/Quality-Score.pdf (modified) (previous)
• doc/theorie/Quality-Score/Quality-Score.synctex.gz (modified) (previous)
• doc/theorie/Quality-Score/Quality-Score.tex (modified) (5 diffs)
• setup.py (modified) (3 diffs)
• src/obipython.py (added)

trunk/.pydevproject

@@ -7 +7 @@
 <path>/OBITools/textwrangler</path>
 </pydev_pathproperty>
-<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.6</pydev_property>
-<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Python-2.6</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Python2.7</pydev_property>
 </pydev_project>

trunk/.settings/org.eclipse.core.resources.prefs

@@ -1 @@
-#Mon Jun 08 09:41:56 CEST 2009
+#Tue Oct 25 23:50:16 ICT 2011
 eclipse.preferences.version=1
+encoding//doc/sphinx/source/conf.py=utf-8
 encoding//src/jwarcher2tab.py=iso-8859-1
 encoding//src/obitools/carto/__init__.py=latin1

trunk/MANIFEST.in

@@ +1 @@
+include setup.py
 recursive-include src *.pyx *.pxd *.c *.h
 

trunk/doc/sphinx/source/optionsSet/sequenceFilter.txt

@@ -18 +18 @@
                         identifier of the sequence. The pattern is case
                         sensitive
+                        
+.. cmdoption::  --id-list=<FILENAME>
+
+                        a file containing a list of sequence identifiers to
+                        be selected.
                         
 .. cmdoption::  -a <ATTRIBUTE_NAME>:<REGULAR_PATTERN>, --attribute=<ATTRIBUTE_NAME>:<REGULAR_PATTERN>

trunk/doc/theorie/Quality-Score/Quality-Score.aux

@@ -1 +1 @@
 \relax 
-\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces default}}{1}}
-\newlabel{defaulttable}{{}{1}}
-\@writefile{lot}{\contentsline {table}{\numberline {2}{\ignorespaces default}}{2}}
-\newlabel{defaulttable}{{}{2}}
+\catcode`:\active
+\catcode`;\active
+\catcode`!\active
+\catcode`?\active
+\select@language{french}
+\@writefile{toc}{\select@language{french}}
+\@writefile{lof}{\select@language{french}}
+\@writefile{lot}{\select@language{french}}
+\@writefile{toc}{\contentsline {section}{\numberline {1}La fonction de score}{1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {1.1}notation}{1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {1.2}Score d'un match dans l'alignement}{1}}
+\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces cas d'un match AA apparent}}{1}}
+\newlabel{defaulttable}{{1.2}{1}}
+\@writefile{lot}{\contentsline {table}{\numberline {2}{\ignorespaces cas d'un mismatch AC apparent}}{2}}
+\newlabel{defaulttable}{{1.2}{2}}

trunk/doc/theorie/Quality-Score/Quality-Score.tex

@@ -4 +4 @@
 %\geometry{landscape}                % Activate for for rotated page geometry
 %\usepackage[parfill]{parskip}    % Activate to begin paragraphs with an empty line rather than an indent
+\usepackage[french]{babel}
+\usepackage[T1]{fontenc}
+\usepackage[latin1]{inputenc}
 \usepackage{graphicx}
 \usepackage{amssymb}
@@ -10 +13 @@
 \DeclareGraphicsRule{.tif}{png}{.png}{`convert #1 `dirname #1`/`basename #1 .tif`.png}
 
-\title{Brief Article}
+\title{Algorithme de micro assemblage entre les lectures pair-end}
 \author{The Author}
 %\date{}                                           % Activate to display a given date or no date
@@ -16 +19 @@
 \begin{document}
 \maketitle
-%\section{}
-%\subsection{}
+
+\section{La fonction de score}
+
+\subsection{notation}
+
+\begin{itemize}
+\item[$P_{X}$ :] probabilité de la base lue sur la séquence X
+\item[$P_{Y}$ :] probabilité de la base lue sur la séquence Y
+\end{itemize}
+
+$P_{X}$ et $P_{Y}$ sont liés au score de la base donnée par le séquenceur. Approximativement par la relation suivante (varie en fonction du schéma de score).
+
+\begin{equation}
+P_{\text{base lue}}= 1 - e^{-\frac{Q}{10}}
+\end{equation}
+
+Pour les Solexa, le type d'erreur prise en compte est une substitution. Nous ne considérons que ce séquenceur et posons que l'erreur à pu se produite de manière équivalente vers toutes les autres bases.
+
+\begin{itemize}
+\item[$S_{match}$ :] score d'un match plein entre deux nucléotides ($S_{match} > 0 $)
+\item[$S_{mismatch}$ :] score d'un mismatch plein entre deux nucléotides ($S_{match} < 0 $)
+\end{itemize}
+
+
+
+\subsection{Score d'un match dans l'alignement}
+
+Le score d'un match (ou d'un mismatch) est en fait la somme d'une fraction d'un match plein et d'une fraction d'un mismatch.
+
+
 
 \begin{table}[htdp]
@@ -29 +60 @@
                 T & $P_{Y}.(1-P_{X})/3$ & $(1-P_{X})/3.(1-P_{Y})/3$ & $(1-P_{X})/3.(1-P_{Y})/3$ & $\mathbf{(1-P_{X})/3.(1-P_{Y})/3}$ \\\hline 
 \end{tabular}
-\caption{default}
+\caption{cas d'un match AA apparent}
 \end{center}
 \label{defaulttable}
@@ -83 +114 @@
                 T & $(1-P_{X})/3.(1-P_{Y})/3$ & $P_{Y}.(1-P_{X})/3$ & $(1-P_{X})/3.(1-P_{Y})/3$ & $\mathbf{(1-P_{X})/3.(1-P_{Y})/3}$ \\\hline 
 \end{tabular}
-\caption{default}
+\caption{cas d'un mismatch AC apparent}
 \end{center}
 \label{defaulttable}

trunk/setup.py

@@ -6 +6 @@
 
 
-from distutils.core import setup
+try:
+   from setuptools.core import setup
+except ImportError:
+   from distutils.core import setup
 from distutils.extension import Extension
 from distutils.util import convert_path
@@ -195 +198 @@
     
 
-VERSION = '0.2.300'
+VERSION = '0.2.400'
 AUTHOR  = 'Eric Coissac'
 EMAIL   = 'eric@coissac.eu'
@@ -237 +240 @@
       packages=findPackage(SRC),
       cmdclass = {'build_ext': build_ext,'build_scripts':build_scripts, 'install_scripts':install_scripts},
-      requires=['Cython (>=0.12)'],
+      requires=['Cython (>=0.16)'],
       zip_safe = False,
       ext_modules=EXTENTION)