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-h, --help
Shows this help message and exits.
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--outname
Output basename of the generated FASTA file(s).
(default: Automatically built from the GFF filename and requested features).
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--features_include
Genomic features or annotation patterns to be searched for ORF selection.
ORFs whose annotations match the entered patterns or genomic features are written in the output FASTA file.
(default: All genomic features present in the input GFF, consequently all annotated ORFs will be written in the output GFF file).
(See the ORFget section for more details).
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--features_exclude
Genomic features or annotation patterns to be searched for ORF exclusion.
ORFs whose annotations match the entered patterns or genomic features are not written in the output FASTA file.
(default: None, consequently all annotated ORFs will be written in the output GFF file).
(See the ORFget section for more details).
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--chr_exclude
To exclude a (or a subset of) seqID(s) from the ORF extraction.
ORFs belonging to these seqIDs (usually chromosomes or contigs) will not be written in the output FASTA file.
(default: None).
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--N
Number of ORFs randomly selected for writing, according to their genomic feature or pattern.
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--type
Sequences type of output (prot (default) / nucl / both).
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--check
DO NOT write sequences that DO NOT finish with a STOP codon.
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--elongate
Number of nucleotides to elongate towards 5' & 3' UTR.