Commit 0b34ddf5 by Eric Coissac

push the first beta version 0.1

parent 57288340
0.1.0a1
\ No newline at end of file
0.1.0b1
\ No newline at end of file
......@@ -9,9 +9,9 @@ Org.Asm: |Orgasm|
Contents:
.. toctree::
:maxdepth: 3
:maxdepth: 2
install
install
strategies
oa
mitochondrion
......
......@@ -119,4 +119,4 @@ From the directory where you retrieved the sources, execute the following comman
> python3 setup.py --serenity install
Once installed, you can test your installation by running the commands of the
:doc:`tutorials <./tutorials>`.
:doc:`tutorials <./mitochondrion>`.
......@@ -446,11 +446,13 @@ prefix indicated as second parametter.
tools accepting the Graph Modeling Language (`GML`_) format. For this
purpose we are usualy using the `Yed <yed>`_ program.
The ``butterfly.mito.intermediate.gml`` file is produced regularly during
the assembling process by the :ref:`oa index <oa_index>` command. It gives
oportunity for following the assembling process during its computation.
The :download:`butterfly.mito.intermediate.gml <../../../samples/butterfly.mito.intermediate.gml>`
file is produced regularly during the assembling process by the
:ref:`oa index <oa_index>` command. It gives opportunity for following
the assembling process during its computation.
The ``butterfly.mito.gml`` contains the final assembling graph.
The :download:`butterfly.mito.gml <../../../samples/butterfly.mito.gml>`
contains the final assembling graph.
These files are produced for the user convinience and they are not
reuse latter by the assembler.
......@@ -533,6 +535,12 @@ relationship.
Compacting graph 100.0 % |#################################################\ ] remain : 00:00:00
Minimum stem coverage = 393
On such assembling graph each contig can be assimilated to a path linking a
subset of vertices of a connected componante. Exploring connecting componante
can by expensive in computation time. To increase our change to find a solution
a heuristic is applyed on the graph to identify the connected componantes that
have a good chance to correspond to the targeted genome.
.. code-block:: bash
2015-08-17 12:25:19,786 [INFO ] Select the good connected componantes
......@@ -541,16 +549,27 @@ relationship.
Coverage 1x = 396
Path is circular
The selected componante(s) is/are analyzed to find an optimal path in them
and the corresponding sequence is printed out in a fasta file. If you look at
the file now contained by the current folder
.. code-block:: bash
ls -l
You can observe two new files.
.. code-block:: bash
-rw-r--r-- 1 coissac staff 31087 17 aoû 12:25 butterfly.mito.fasta
-rw-r--r-- 1 coissac staff 252144 17 aoû 12:25 butterfly.mito.path.gml
The :download:`butterfly.mito.path.gml <../../../samples/butterfly.mito.path.gml>`
file contains a simplified graph representation of the assembling similar to the
one produced by the :ref:`oa buildgraph <oa_buildgraph>` command but including
moreover information about the selected path.
.. figure:: butterfly.mito.path.*
:align: center
:figwidth: 80 %
......@@ -561,7 +580,11 @@ relationship.
It can be visualized using the `Yed <yed>`_ program
butterfly.mito.path
The :download:`butterfly.mito.fasta <../../../samples/butterfly.mito.fasta>`
file contains the produced sequence in fasta format. Most of the time you have
a single contig corresponding to the complete sequence of the targeted genome.
You can read this file using your favorite sequence/text editor or using the
**Unix** ``cat`` command.
.. code-block:: bash
......
......@@ -3,6 +3,10 @@
The ORGanelle ASseMbler command line
====================================
|Orgasm| is run using the :ref:`oa <oa>` Unix command. It is providing
a set of sub-commands allowing for the complete assembling of small genomes
(organelle genomes) from a genome skimming sequence dataset. You can have a
basic idea on how to proced by following the :doc:`tutorial <./mitochondrion>`.
The ORGanelle ASseMbler commands
--------------------------------
......@@ -12,7 +16,7 @@ The ORGanelle ASseMbler commands
:figwidth: 80 %
:width: 500
The :ref:`organelle assembler <oa>`'s proides a set of commands.
The :ref:`organelle assembler <oa>`'s provides a set of commands.
Several of these commands (at least three) have to executed to complete
an assembling process.
......@@ -27,6 +31,9 @@ The ORGanelle ASseMbler commands
assembling but sometime useful to get or restore some information.
The set of sub-commands can be splitted in several categories corresponding to
the main steps of the assembling procedure.
.. toctree::
:maxdepth: 2
......
major = 0
minor = '1'
serial= '0a0'
serial= '0b1'
version = "%2d.%s.%s" % (major,minor,serial)
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment