Commit 1270b36d by Eric Coissac

Corresponds to the new version of OBITools tagged 1.00.006 deposited on PyPI

parent 3a4abd9c
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
<?eclipse-pydev version="1.0"?><pydev_project> <?eclipse-pydev version="1.0"?><pydev_project>
<pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH"> <pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
<path>/OBITools-1.0/src</path> <path>/OBITools-1.0/src</path>
<path>/OBITools-1.0/textwrangler</path> <path>/${PROJECT_DIR_NAME}/distutils.ext</path>
</pydev_pathproperty> </pydev_pathproperty>
<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</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_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Python2.7</pydev_property>
......
...@@ -39,8 +39,8 @@ class littlebigman(build_exe): ...@@ -39,8 +39,8 @@ class littlebigman(build_exe):
# self.ctools = self.distribution.ctools # self.ctools = self.distribution.ctools
if os.path.isfile("src/littlebigman.c"): if os.path.isfile("distutils.ext/src/littlebigman.c"):
self.executables = [('littlebigman',{"sources":["src/littlebigman.c"]})] self.executables = [('littlebigman',{"sources":["distutils.ext/src/littlebigman.c"]})]
self.check_executable_list(self.executables) self.check_executable_list(self.executables)
else: else:
self.executables = [] self.executables = []
......
...@@ -35,8 +35,8 @@ class pidname(build_exe): ...@@ -35,8 +35,8 @@ class pidname(build_exe):
# self.ctools = self.distribution.ctools # self.ctools = self.distribution.ctools
if os.path.isfile("src/pidname.c"): if os.path.isfile("distutils.ext/src/pidname.c"):
self.executables = [('pidname',{"sources":["src/pidname.c"]})] self.executables = [('pidname',{"sources":["distutils.ext/src/pidname.c"]})]
self.check_executable_list(self.executables) self.check_executable_list(self.executables)
else: else:
self.executables = [] self.executables = []
......
obiclean_cluster obiclean_cluster
================ ================
An associative array indicating to which cluster each sequence is associated in each sample A boolean value set to True if the sequence has the `head` status in at least one sample.
.. seealso:: .. seealso::
......
...@@ -20,6 +20,8 @@ amino-acids. ...@@ -20,6 +20,8 @@ amino-acids.
fasta fasta
fastq fastq
attributes attributes
..
genbank genbank
embl embl
...@@ -37,18 +39,19 @@ either a directory containing all :doc:`NCBI taxonomy dump files <./taxdump>` or ...@@ -37,18 +39,19 @@ either a directory containing all :doc:`NCBI taxonomy dump files <./taxdump>` or
taxdump taxdump
obitaxonomy obitaxonomy
The ecoPCR files ..
---------------- The ecoPCR files
----------------
ecoPCR_ simulates a PCR experiment by selecting in a sequence database, sequences matching
simultaneously two primers sequences in a way allowing a PCR amplification of a DNA region. ecoPCR_ simulates a PCR experiment by selecting in a sequence database, sequences matching
simultaneously two primers sequences in a way allowing a PCR amplification of a DNA region.
The ecoPrimers files
-------------------- The ecoPrimers files
--------------------
The OBITools files
------------------ The OBITools files
------------------
.. _ecoPCR: http://www.grenoble.prabi.fr/trac/ecoPCR .. _ecoPCR: http://www.grenoble.prabi.fr/trac/ecoPCR
......
...@@ -19,6 +19,5 @@ Indices and tables ...@@ -19,6 +19,5 @@ Indices and tables
================== ==================
* :ref:`genindex` * :ref:`genindex`
* :ref:`genindex`
* :ref:`search` * :ref:`search`
...@@ -26,15 +26,11 @@ Availability of the ``OBITools`` ...@@ -26,15 +26,11 @@ Availability of the ``OBITools``
................................ ................................
The ``OBITools`` are open source and protected by the CeCILL 2.1 license The ``OBITools`` are open source and protected by the CeCILL 2.1 license
(`http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html <http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html>`_). All the sources (`http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html <http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html>`_).
can be downloaded from our subversion server
(`http://www.grenoble.prabi.fr/public-svn/OBISofts/OBITools <http://www.grenoble.prabi.fr/public-svn/OBISofts/OBITools>`_). The ``OBITools`` are The ``OBITools`` are deposited on the Python Package Index (PyPI : `https://pypi.python.org/pypi/obitools <https://pypi.python.org/pypi/obitools>`_)
deposited on the Python package index (`https://pypi.python.org/pypi/obitools <https://pypi.python.org/pypi/obitools>`_) and all the sources can be downloaded from our subversion server
and therefore the easiest way to install the ``OBITools`` is to use the python package installers (`http://www.grenoble.prabi.fr/public-svn/OBISofts/OBITools <http://www.grenoble.prabi.fr/public-svn/OBISofts/OBITools>`_).
`pip` (`https://pypi.python.org/pypi/pip <https://pypi.python.org/pypi/pip>`_) that will take in charge the installation of the other
dependencies. If you have not ``pip`` installed on your computer, please visite the
following page: `http://pip.readthedocs.org/en/latest/installing.html <http://pip.readthedocs.org/en/latest/installing.html>`_ . Python 2.7, and a C compiler
have to be installed prior to the ``OBITools``.
Prerequisites Prerequisites
............. .............
...@@ -47,24 +43,125 @@ system: ...@@ -47,24 +43,125 @@ system:
* ``gcc`` (installed by default on most ``Unix`` systems, available from the * ``gcc`` (installed by default on most ``Unix`` systems, available from the
GNU sites dedicated to `GCC <https://www.gnu.org/software/gcc/>`_ and GNU sites dedicated to `GCC <https://www.gnu.org/software/gcc/>`_ and
`GMake <https://www.gnu.org/software/make/>`_) `GMake <https://www.gnu.org/software/make/>`_)
On a linux system
^^^^^^^^^^^^^^^^^
You have to take care that the Python-dev packages are installed.
On MacOSX
^^^^^^^^^
The C compiler and all the other compilation tools are included in the `XCode <https://itunes.apple.com/fr/app/xcode/id497799835?mt=12>`_
application not installed by default. The Python included in the system is not
suitable for running the ``OBITools``. You have to install a complete distribution
of Python that you can download as a `MacOSX package from the Python website <https://www.python.org/downloads/>`_.
User level installation
.......................
There is two main ways for installing the ``OBITools``. The easiest one is to install them
using the :download:`get_obitools.py <../../../get_obitools/get_obitools.py>` script.
Once downloaded, move the file :download:`get_obitools.py <../../../get_obitools/get_obitools.py>` in the directory where you want to install
the ``OBITools``. From a Unix terminal you must now run the command :
.. code-block:: bash
If you want to compile by yourself the ``OBITools``, you will need to install futhermore: > python get_obitools.py
The script will create a new directory at the place you are running it in which all the
``OBITools`` will be installed. No system privilege are required, and you system will not
be altered in any way by the obitools installation.
The newly created directory is named OBITools-VERSION where version is substituted by the
latest version number available.
Inside the newly created directory all the ``OBITools`` are installed. Close to this directory
there is a shell script named ``obitools``. Running this script activate the ``OBITools``
by reconfiguring your Unix environment.
.. code-block:: bash
> ./obitools
* Cython (available from the `Cython website <http://http://cython.org/>`_) Once activated you can desactivate the ``OBITools`` byt typing the command ``exit``.
* any subversion client (a list of clients is avalaible from
`Wikipedia <http://en.wikipedia.org/wiki/Comparison_of_Subversion_clients>`_) .. code-block:: bash
> exit
OBITools are no more activated, Bye...
======================================
System level installation
.........................
As all the Python software deposited on `PyPI <https://pypi.python.org/pypi/obitools>`_, ``OBITools`` can be
installed using the `pip` (`https://pypi.python.org/pypi/pip <https://pypi.python.org/pypi/pip>`_) command.
We recommand to use `pip` over `easy_install` as python package manager.
If you have not ``pip`` installed on your computer, please visite the
following page: `http://pip.readthedocs.org/en/latest/installing.html <http://pip.readthedocs.org/en/latest/installing.html>`_ .
Remember that Python 2.7, and a C compiler have to be installed before the ``OBITools``.
To install ``OBITools`` you have first to install dependencies
.. code-block:: bash
> pip install -U virtualenv
> pip install -U sphinx
> pip install -U cython
You can now install ``OBITools`` themselves.
.. code-block:: bash
> pip install -U obitools
Perhaps that on your system, the system administrator privilege are required to realise
these installations. If you are yourself administrator of your computer run the above commands
with the ``sudo`` command in front.
.. code-block:: bash
> sudo pip install -U virtualenv
> sudo pip install -U sphinx
> sudo pip install -U cython
> sudo pip install -U obitools
Retrieving the sources of the OBITools Retrieving the sources of the OBITools
...................................... ......................................
If you want to compile by yourself the ``OBITools``, you will need to install the same
prerequisite:
.. code-block:: bash
> pip install -U virtualenv
> pip install -U sphinx
> pip install -U cython
moreover you need to install any subversion client (a list of clients is available from `Wikipedia <http://en.wikipedia.org/wiki/Comparison_of_Subversion_clients>`_)
Then you can download the
.. code-block:: bash .. code-block:: bash
> svn co http://www.grenoble.prabi.fr/public-svn/OBISofts/OBITools/trunk OBITools > svn co http://www.grenoble.prabi.fr/public-svn/OBISofts/OBITools/branches/OBITools-1.00/ OBITools
This command will create a new directory called ``OBITools``. This command will create a new directory called ``OBITools``.
Compiling and installing the Obitools Compiling and installing the ``OBITools``
..................................... .........................................
From the directory where you retrieved the sources, execute the following commands: From the directory where you retrieved the sources, execute the following commands:
...@@ -85,7 +182,7 @@ Introduction ...@@ -85,7 +182,7 @@ Introduction
DNA metabarcoding is an emerging approach for biodiversity studies (Taberlet et DNA metabarcoding is an emerging approach for biodiversity studies (Taberlet et
al. 2012). Originally mainly developed by microbiologists (e.g. Sogin et al. al. 2012). Originally mainly developed by microbiologists (e.g. Sogin et al.
2006), it is now widely used for plants (e.g. Sønstebø et al. 2010, Parducci et 2006), it is now widely used for plants (e.g. Sonstebo et al. 2010, Parducci et
al. 2012, Yoccoz et al. 2012) and animals from meiofauna (e.g. Chariton et al. al. 2012, Yoccoz et al. 2012) and animals from meiofauna (e.g. Chariton et al.
2010, Baldwin et al. 2013) to larger organisms (e.g. Andersen et al. 2012, 2010, Baldwin et al. 2013) to larger organisms (e.g. Andersen et al. 2012,
Thomsen et al. 2012). Interestingly, this method is not limited to *sensu Thomsen et al. 2012). Interestingly, this method is not limited to *sensu
...@@ -131,7 +228,7 @@ records based on the taxonomy. ...@@ -131,7 +228,7 @@ records based on the taxonomy.
References References
.......... ..........
Andersen K, Bird KL, Rasmussen M, Haile J, Breuning-Madsen H, Kjær KH, Orlando Andersen K, Bird KL, Rasmussen M, Haile J, Breuning-Madsen H, Kjr KH, Orlando
L, Gilbert MTP, Willerslev E (2012) Meta-barcoding of "dirt" DNA from soil L, Gilbert MTP, Willerslev E (2012) Meta-barcoding of "dirt" DNA from soil
reflects vertebrate biodiversity. Molecular Ecology, 21, 1966-1979. reflects vertebrate biodiversity. Molecular Ecology, 21, 1966-1979.
...@@ -154,7 +251,7 @@ Frontiers in Ecology and the Environment, 8, 233-238. ...@@ -154,7 +251,7 @@ Frontiers in Ecology and the Environment, 8, 233-238.
Deagle BE, Kirkwood R, Jarman SN (2009) Analysis of Australian fur seal diet by Deagle BE, Kirkwood R, Jarman SN (2009) Analysis of Australian fur seal diet by
pyrosequencing prey DNA in faeces. Molecular Ecology, 18, 2022-2038. pyrosequencing prey DNA in faeces. Molecular Ecology, 18, 2022-2038.
Kowalczyk R, Taberlet P, Coissac E, Valentini A, Miquel C, Kaminski T, Wójcik JM Kowalczyk R, Taberlet P, Coissac E, Valentini A, Miquel C, Kaminski T, Wjcik JM
(2011) Influence of management practices on large herbivore diet - case of (2011) Influence of management practices on large herbivore diet - case of
European bison in Bialowieza Primeval Forest (Poland). Forest Ecology and European bison in Bialowieza Primeval Forest (Poland). Forest Ecology and
Management, 261, 821-828. Management, 261, 821-828.
...@@ -181,7 +278,7 @@ GJ (2006) Microbial diversity in the deep sea and the underexplored "rare ...@@ -181,7 +278,7 @@ GJ (2006) Microbial diversity in the deep sea and the underexplored "rare
biosphere". Proceedings of the National Academy of Sciences of the United States biosphere". Proceedings of the National Academy of Sciences of the United States
of America, 103, 12115-12120. of America, 103, 12115-12120.
Sønstebø JH, Gielly L, Brysting A, Reidar E, Edwards M, Haile J, Willerslev E, S�nsteb� JH, Gielly L, Brysting A, Reidar E, Edwards M, Haile J, Willerslev E,
Coissac E, Rioux D, Sannier J, Taberlet P, Brochmann C (2010) Using Coissac E, Rioux D, Sannier J, Taberlet P, Brochmann C (2010) Using
next-generation sequencing for molecular reconstruction of past Arctic next-generation sequencing for molecular reconstruction of past Arctic
vegetation and climate. Molecular Ecology Resources, 10, 1009-1018. vegetation and climate. Molecular Ecology Resources, 10, 1009-1018.
...@@ -198,8 +295,8 @@ Cruaud C, Nascetti G, Wincker P, Swenson JE, Taberlet P (2009) New perspectives ...@@ -198,8 +295,8 @@ Cruaud C, Nascetti G, Wincker P, Swenson JE, Taberlet P (2009) New perspectives
in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL
approach. Molecular Ecology Resources, 9, 51-60. approach. Molecular Ecology Resources, 9, 51-60.
Yoccoz NG, Bråthen KA, Gielly L, Haile J, Edwards ME, Goslar T, von Stedingk H, Yoccoz NG, Brthen KA, Gielly L, Haile J, Edwards ME, Goslar T, von Stedingk H,
Brysting AK, Coissac E, Pompanon F, Sønstebø JH, Miquel C, Valentini A, de Bello Brysting AK, Coissac E, Pompanon F, S�nsteb� JH, Miquel C, Valentini A, de Bello
F, Chave J, Thuiller W, Wincker P, Cruaud C, Gavory F, Rasmussen M, Gilbert MTP, F, Chave J, Thuiller W, Wincker P, Cruaud C, Gavory F, Rasmussen M, Gilbert MTP,
Orlando L, Brochmann C, Willerslev E, Taberlet P (2012) DNA from soil mirrors Orlando L, Brochmann C, Willerslev E, Taberlet P (2012) DNA from soil mirrors
plant taxonomic and growth form diversity. Molecular Ecology, 21, 3647-3655. plant taxonomic and growth form diversity. Molecular Ecology, 21, 3647-3655.
...@@ -324,7 +421,7 @@ A), pp. 13-31. Springer Science+Business Media, New York. ...@@ -324,7 +421,7 @@ A), pp. 13-31. Springer Science+Business Media, New York.
Cornish-Bowden A (1985) Nomenclature for incompletely specified bases in nucleic Cornish-Bowden A (1985) Nomenclature for incompletely specified bases in nucleic
acid sequences: recommendations 1984. Nucleic Acids Research, 13, 3021-3030. acid sequences: recommendations 1984. Nucleic Acids Research, 13, 3021-3030.
Ficetola GF, Coissac E, Zundel S, Riaz T, Shehzad W, Bessière J, Taberlet P, Ficetola GF, Coissac E, Zundel S, Riaz T, Shehzad W, Bessire J, Taberlet P,
Pompanon F (2010) An in silico approach for the evaluation of DNA barcodes. BMC Pompanon F (2010) An in silico approach for the evaluation of DNA barcodes. BMC
Genomics, 11, 434. Genomics, 11, 434.
......
...@@ -14,6 +14,8 @@ After extracting DNA from the faeces, the DNA amplifications were carried out us ...@@ -14,6 +14,8 @@ After extracting DNA from the faeces, the DNA amplifications were carried out us
primers TTAGATACCCCACTATGC and TAGAACAGGCTCCTCTAG amplifiying the 12S-V5 region primers TTAGATACCCCACTATGC and TAGAACAGGCTCCTCTAG amplifiying the 12S-V5 region
(Riaz et al. 2011), together with a wolf blocking oligonucleotide. (Riaz et al. 2011), together with a wolf blocking oligonucleotide.
The complete data set can be downloaded here: :download:`the tutorial dataset<../../../wolf_tutorial.zip>`
+-------------------------------------------------------------+ +-------------------------------------------------------------+
| Good to remember: I am working with tons of sequences | | Good to remember: I am working with tons of sequences |
......
...@@ -4127,6 +4127,45 @@ AD1LQ0UOryaXbwAAAM8AAAAOABgAAAAAAAEAAACkgemOAwBzdm4vdXRpbGl0eS5weVVUBQADhk8u ...@@ -4127,6 +4127,45 @@ AD1LQ0UOryaXbwAAAM8AAAAOABgAAAAAAAEAAACkgemOAwBzdm4vdXRpbGl0eS5weVVUBQADhk8u
VHV4CwABBPUBAAAEFAAAAFBLBQYAAAAAEwATAHMGAACgjwMAAAA=\ VHV4CwABBPUBAAAEFAAAAFBLBQYAAAAAEwATAHMGAACgjwMAAAA=\
""" """
install_script="""\
#!/bin/bash
binpath=%s/bin
system=`uname -s`
if [ "$system" == "Darwin" ]
then
loginshell=`dscl . -read /Users/\`whoami\` UserShell | awk '{print $NF}'`
parent=`$binpath/pidname $PPID | awk '{print $NF}'`
else
loginshell=`getent passwd \`whoami\` | awk -F ':' '{print $NF}'`
parent=`readlink /proc/$PPID/exe`
fi
if [[ "$parent" == *"login" ]]
then
target=$loginshell
else
target=$parent
fi
if [[ "$target" == *"csh" ]]
then
echo "Welcome in OBITools"
activate="$binpath/activate.csh"
else
activate="$binpath/activate"
fi
$target -c "source $activate; $target"
echo
echo OBITools are no more activated, Bye...
echo ======================================
echo
"""
PIP_MINVERSION = '1.5' PIP_MINVERSION = '1.5'
local_pip=[] local_pip=[]
...@@ -4283,15 +4322,7 @@ def main(): ...@@ -4283,15 +4322,7 @@ def main():
python = os.path.join(binpath,'python') python = os.path.join(binpath,'python')
with open(activate,"w") as fp: with open(activate,"w") as fp:
print >>fp,"#!%s" % python print >>fp, install_script % virtualenvname
print >>fp
print >>fp,"import os"
print >>fp,"ppid = os.getppid()"
print >>fp,"if os.path.islink('/proc/%d/exe' % ppid):"
print >>fp,' shell = os.path.realpath("/proc/%d/exe" % ppid)'
print >>fp,"else:"
print >>fp,"os.environ['PATH']='%s:%s' % (binpath,os.environ['PATH'])"
print >>fp,"os.execlp(shell,shell)"
print >>fp print >>fp
st = os.stat(activate) st = os.stat(activate)
......
...@@ -19,7 +19,7 @@ from os import path ...@@ -19,7 +19,7 @@ from os import path
PACKAGE = "OBITools" PACKAGE = "OBITools"
VERSION = "1.0.005" VERSION = "1.0.006"
AUTHOR = 'Eric Coissac' AUTHOR = 'Eric Coissac'
EMAIL = 'eric@coissac.eu' EMAIL = 'eric@coissac.eu'
URL = 'metabarcoding.org/obitools' URL = 'metabarcoding.org/obitools'
......
...@@ -398,6 +398,9 @@ if __name__ == '__main__': ...@@ -398,6 +398,9 @@ if __name__ == '__main__':
node['obiclean_singletoncount']=s node['obiclean_singletoncount']=s
node['obiclean_samplecount']=s+i+h node['obiclean_samplecount']=s+i+h
if 'obiclean_head' not in node:
node['obiclean_head']=False
if (not options.clustermode): if (not options.clustermode):
del node["obiclean_status"] del node["obiclean_status"]
......
major = 1 major = 1
minor = 0 minor = 0
serial= '005' serial= '006'
version = "%2d.%02d %s" % (major,minor,serial) version = "%2d.%02d %s" % (major,minor,serial)
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