INCLUDED FILES:
validate_gtf.pl The GTF validator.
eval.pl The Eval GUI. evaluate_gtf.pl The command line interface to the Evaluate function. get_general_stats.pl The command line interface to the GenStats function. filter_gtfs.pl The command line interface to the Filter function. graph_gtfs.pl The command line interface to the Graph function. get_overlap_stats.pl The command line interface to the Overlap function. get_distribution.pl The command line interface to the Dist function.
GTF.pm A Perl library for dealing with GTF files. Eval.pm A Perl library containing all the Eval functions.
eval-documentation.pdf The complete Eval documentation including a user guide and code documentation. eval-summary.pdf A summary of the Eval system.
Also included are three gtf files containing annotation of the NCBI build 31 / November 2002 Golden Path human chromosome 22. A fasta file of the genomic sequence is available for download from genome.ucsc.edu.
chr22.twinscan.gtf chr22.genscan.gtf chr22.refseq.gtf
REQUIREMENTS:
The Eval system requires Perl 5.0 or later and Perl::Tk 8.0 or later. The Perl::Tk module can be found at www.cpan.org. To display graphs from the GUI the gnuplot utility is required. gnplot can be found at www.gnuplot.info.
INSTALLATION:
To install the Eval package just unpack the files to any directory. The library files (*.pm files) should be placed in a directory in the users Perl library path. For example, if the *.pm files are located in /usr/lib/eval, then the Perl library path should include /usr/lib/eval:
PERL5LIB=/usr/lib:/usr/lib/eval
Alternatively the files may all be placed in a single directory, which will allow the programs to be run only from that directory.
Correct installation can be tested using the three provided GTF files. The command:
eval.pl -v chr22.refseq.gtf chr22.twinscan.gtf chr22.genscan.gtf
should load the three files in the GUI without any errors if the libraries have been installed correctly.
USE:
See the documentation for a detailed description of how to use the programs.