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PARSEVAL(1) User Commands PARSEVAL(1)


parseval - comparative analysis of two alternative sources of annotation


parseval [options] reference.gff3 prediction.gff3


Basic options:

Print debugging messages
Print help message and exit
Extend gene loci by this many nucleotides; default is 0
Print verbose warning messages
Print version number and exit
Output options:
Location from which to copy shared data for HTML output (if `make install' has not yet been run)
Indicate desired output format; possible options: 'csv', 'text', or 'html' (default='text'); in 'text' or 'csv' mode, will create a single file; in 'html' mode, will create a directory
Do no print GFF3 output corresponding to each comparison
File/directory to which output will be written; default is the terminal (STDOUT)
In HTML output mode, skip generation of PNG graphics for each gene locus
Only print summary statistics, do not print individual comparisons
Force overwrite of any existing output files
Optional label for reference annotations
Optional label for prediction annotations
Filtering options:
Create a default configuration file for filtering reported results and quit, performing no comparisons
Use the indicated configuration file to filter reported results;
Maximum transcripts allowed per locus; use 0 to disable limit; default is 32
January 2016 parseval 0.15.1