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README.old
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HDFPerl version 0.10
====================
The README is used to introduce the module and provide instructions on
how to install the module, any machine dependencies it may have (for
example C compilers and installed libraries) and any other information
that should be provided before the module is installed.
A README file is required for CPAN modules since CPAN extracts the
README file from a module distribution so that people browsing the
archive can use it get an idea of the modules uses. It is usually a
good idea to provide version information here so that people can
decide whether fixes for the module are worth downloading.
INSTALLATION
To install this module type the following:
Modify Makefile.PL so that it points to the location of the HDF5 library
perl Makefile.PL LIB=/install_path
make
make install
That will put all the files in that directory. In order to use modules that are
stored in that location, you will need to add the following like to your Perl
programs:
use lib "/install_path"
EXAMPLES
There are two example scripts in the distribution along with sample data files:
fasta2hdf5.pl and BioHDF_example.pl. BEFORE EXECUTING THE SCRIPTS, MAKE SURE
TO SPECIFY THE INSTALLATION PATH ON THEM.
fasta2hdf5.pl migrates sequence data from a FASTA file into an HDF5 file using
Perl wrappers for HDF5 functions. This script can be executed as follows:
./fasta2hdf5.pl sequences.fasta sequences.h5
where sequences.fasta is the FASTA file and sequences.h5 is the resulting HDF5
file.
Bio_HDF_Perl.pl also migrates data from a FASTA file into an HDF5 file but
this time using high level APIs. The script also performs sorting on the data
and sequences searches in the HDF5 file. To execute the script just type:
./BioHDF_example.pl
The script reads the files FACTORVII_01.fsa and FACTORVIII_01.qual containing
bases and quality values, and migrates the data into the file FACTORVIII_01.h5.
The script displays the number of records processed, an identifier for a
particular sequence record to search, and the respective data for the found
sequence
The resulting HDF5 files can be viewed through the hdfviewer or h5dump.
DEPENDENCIES
This module requires these other modules and libraries:
hdf5
Modifications need to be made to the Makefile.PL file.
'LIBS' variable should point to the hdf5 library installation directory (lib)
'INC' variable should point to the hdf5 header installation directory (include)