The script aims to filter isoforms when present. For a locus: - when all isoforms have CDS we keep the one with the longest CDS. - when some isoforms have CDS some others not, we keep the one with the longest CDS. - when none of the isoforms have CDS, we keep the one with the longest concatenated exons.
agat_sp_keep_longest_isoform.pl -gff file.gff [ -o outfile ]
--gff or -f
--output or -o
File where will be written the result. If no output file is specified, the output will be written to STDOUT.
-c or --config
String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
-h or --help
Display this helpful text.