The script reads a gff annotation file, and create two output files, one contains the gene models with ORF passing the test, the other contains the rest. By default the test is "> 100" that means all gene models that have ORF longer than 100 Amino acids, will pass the test.
agat_sp_filter_by_ORF_size.pl --gff infile.gff [ -o outfile ]
agat_sp_filter_by_ORF_size.pl -h
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-g or --gff
Input GTF/GFF file.
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-s or --size
ORF size to apply the test. Default 100.
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-t or --test Test to apply (> < = >= <=). If you us one of these two character >, <, please don't forget to quote you parameter liket that "<=". Else your terminal will complain. By default it will be ">"
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-v
Verbose. Useful for debugging purpose. Bolean
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-o or --out or --output or --outfile
Output GFF file. If no output file is specified, the output will be written to STDOUT.
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-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).
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-h or --help
Display this helpful text.