Sarment
Sarment is a source package of object-oriented Python modules for sequence
segmentation via HMM analysis and Maximal Predictive Partitioning.
Sarment is under GPL license.
It provides several classes:
- data classes to store data such as sequences and vectors,
- count classes to compute counts and proportions of words on sequences,
- partition classes to handle partitions and partitionings,
- Lexique class to compute partitions, either by HMM methods or
maximal partitioning.
Data storage and heavy computation are written in C++, to limit memory
use and time consumption. Then, compilation process is needed to
install Sarment.
Downloading Sarment
04/28/2016: Last version, number 5. All the files for version 4 are here , and for version 3,
here .
Sarment is available for LINUX or MacOS X operating systems.
It needs Python version 2.(>=2).
Makefile is made for GNU make and compilation needs
g++ version >=2.95.
Compilation needs Python headers files. The header files are typically
installed with Python.
- On Linux and Unix, these are located in the directories
prefix/include/pythonversion/ and exec_prefix/include/pythonversion/,
where prefix and exec_prefix are defined by the corresponding
parameters to Python's configure script.
If you have problems, here is an already compilated version of Sarment for
i386 64 bits, python 2.7, in
tar gz
-
On MacOs X, these are located in the directory
/System/Library/Frameworks/Python.framework/Headers.
Normally, they are installed in MacOs X distrib, hence you do not have
anything to do.
Untarify this archive wherever you want, and do not forget to update
PYTHONPATH environment variable.
Sarment sources can be downloaded in
tar gz.
Several headers locations are tested during make operation
(see top of the makefile), but perhaps yours is not included.
In that case, uncomment INC definition and add the correct location.
For compilation, just do "make".
During compilation, a link to the "right"
header directory is made in SrcCPP directory, with name Pythondev. If
the link is not correct, either delete it before recompilating, or
change it to the correct directory.
Afterwards, "make exec" tarifies in Sarment.tar all the files
that are necessary for usage.
Untarify this file wherever you want, and do not forget to update
PYTHONPATH environment variable.
Using Sarment
The version of python to be used depends on your system, which
determines the link of Pythondev in SrcCPP directory.
For the use of these classes, there is a manual in html or pdf .
To facilitate the usage of these classes, there is a tutorial in html or pdf .
Reference
Sarment: Python modules for HMM analysis and partitioning of sequences.
Guéguen, L. Bioinformatics. 2005 Aug 15;21(16):3427-8
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/16/3427?etoc
If you encounter some problems when using Sarment, please contact Laurent
Guéguen. Any comments or suggestions are welcome.
If you have problems
or comments...
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