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OBITools
Commit a12bee70 by Eric Coissac
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patch the installer for easy_install and pip

parent 34389657
Showing with 112 additions and 17 deletions
.pydevproject
......@@ -6,6 +6,6 @@
<path>/OBITools/src</path>
<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>
.settings/org.eclipse.core.resources.prefs
#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
encoding//src/obitools/statistics/hypergeometric.py=UTF-8
MANIFEST.in
include setup.py
recursive-include src *.pyx *.pxd *.c *.h
doc/sphinx/source/optionsSet/sequenceFilter.txt
......@@ -18,6 +18,11 @@ sequence selection options
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>
regular expression pattern matched against the
......
doc/theorie/Quality-Score/Quality-Score.aux
\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}}
doc/theorie/Quality-Score/Quality-Score.tex
......@@ -3,22 +3,54 @@
\geometry{letterpaper} % ... or a4paper or a5paper or ...
%\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}
\usepackage{amsmath} %maths
\usepackage{epstopdf}
\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
\begin{document}
\maketitle
%\section{}
%\subsection{}
\begin{table}[htdp]\begin{center}
\section{La fonction de score}
\subsection{notation}
\begin{itemize}
\item[$P_{X}$ :] probabilit de la base lue sur la squence X
\item[$P_{Y}$ :] probabilit de la base lue sur la squence Y
\end{itemize}
$P_{X}$ et $P_{Y}$ sont lis au score de la base donne par le squenceur. Approximativement par la relation suivante (varie en fonction du schma 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 considrons que ce squenceur et posons que l'erreur pu se produite de manire quivalente vers toutes les autres bases.
\begin{itemize}
\item[$S_{match}$ :] score d'un match plein entre deux nuclotides ($S_{match} > 0 $)
\item[$S_{mismatch}$ :] score d'un mismatch plein entre deux nuclotides ($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]
\begin{center}
\begin{tabular}{|c|c|c|c|c|}
\hline
& A & C & G & T \\\hline
......@@ -27,7 +59,10 @@
G & $P_{Y}.(1-P_{X})/3$ & $(1-P_{X})/3.(1-P_{Y})/3$ & $\mathbf{(1-P_{X})/3.(1-P_{Y})/3}$ & $(1-P_{X})/3.(1-P_{Y})/3$ \\\hline
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}\end{center}\label{defaulttable}\end{table}
\caption{cas d'un match AA apparent}
\end{center}
\label{defaulttable}
\end{table}
\begin{equation}
\begin{array}{rcrcl}
......@@ -68,7 +103,8 @@ S'_{(X=Y)} = \frac{S_{match} + S_{mismatch}}{4}
\end{equation}
\begin{table}[htdp]\begin{center}
\begin{table}[htdp]
\begin{center}
\begin{tabular}{|c|c|c|c|c|}
\hline
& A & C & G & T \\\hline
......@@ -77,7 +113,10 @@ S'_{(X=Y)} = \frac{S_{match} + S_{mismatch}}{4}
G & $(1-P_{X})/3.(1-P_{Y})/3$ & $P_{Y}.(1-P_{X})/3$ & $\mathbf{(1-P_{X})/3.(1-P_{Y})/3}$ & $(1-P_{X})/3.(1-P_{Y})/3$ \\\hline
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}\end{center}\label{defaulttable}\end{table}
\caption{cas d'un mismatch AC apparent}
\end{center}
\label{defaulttable}
\end{table}
\begin{equation}
\begin{array}{rcrcl}
......
setup.py
......@@ -5,7 +5,10 @@
#
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
from distutils import log
......@@ -194,7 +197,7 @@ def findC(root,base=None,pyrexs=None):
return pyrexs
VERSION = '0.2.300'
VERSION = '0.2.400'
AUTHOR = 'Eric Coissac'
EMAIL = 'eric@coissac.eu'
URL = 'www.grenoble.prabi.fr/trac/OBITools'
......@@ -236,7 +239,7 @@ setup(name="OBITools",
package_dir = {'': SRC},
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)
src/obipython.py 0 → 100644
#!/usr/local/bin/python
'''
Created on 23 janv. 2010
@author: coissac
'''
from IPython.Shell import IPShellEmbed
from obitools.interactive import *
try:
import numpy
__with_numpy__=True
except ImportError:
__with_numpy__=False
try:
from matplotlib import *
__with_matplotlib__=True
matplotlib.interactive(True)
from matplotlib.pyplot import *
except ImportError:
__with_matplotlib__=False
obi_ns = dict(
kissa = 15,
koira = 16)
if __name__ == '__main__':
ipshell = IPShellEmbed()
ipshell.set_banner('OBIPython dev version')
ipshell.old_banner2='coucou'
ipshell()
\ No newline at end of file
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