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| PARSEVAL(1) |
User Commands |
PARSEVAL(1) |
NAME¶
parseval - comparative analysis of two alternative sources of annotation
SYNOPSIS¶
parseval [options] reference.gff3 prediction.gff3
DESCRIPTION¶
Basic options:
- -d|--debug:
- Print debugging messages
- -h|--help:
- Print help message and exit
- -l|--delta: INT
- Extend gene loci by this many nucleotides; default is 0
- -V|--verbose:
- Print verbose warning messages
- -v|--version:
- Print version number and exit
- Output options:
- -a|--datashare: STRING
- Location from which to copy shared data for HTML output (if `make install'
has not yet been run)
- -f|--outformat: STRING
- 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
- -g|--nogff3:
- Do no print GFF3 output corresponding to each comparison
- -o|--outfile: FILENAME
- File/directory to which output will be written; default is the terminal
(STDOUT)
- -p|--nopng:
- In HTML output mode, skip generation of PNG graphics for each gene
locus
- -s|--summary:
- Only print summary statistics, do not print individual comparisons
- -w|--overwrite:
- Force overwrite of any existing output files
- -x|--refrlabel: STRING
- Optional label for reference annotations
- -y|--predlabel: STRING
- Optional label for prediction annotations
- Filtering options:
- -k|--makefilter
- Create a default configuration file for filtering reported results and
quit, performing no comparisons
- -r|--filterfile: STRING
- Use the indicated configuration file to filter reported results;
- -t|--maxtrans: INT
- Maximum transcripts allowed per locus; use 0 to disable limit; default is
32
