ExtractFeature extracts parts of the alignment corresponding to certain features.
The features to extract are typically provided via a GFF file.
maf.filter= \ [...] ExtractFeature( \ ref_species=species1, \ feature.file=species1.gff3.gz, \ feature.file.compression=gzip, \ feature.format=GFF, \ feature.type=mRNA, \ compression=gzip, \ complete=yes, \ ignore_strand=no), \ [...]
The name of the species for which the coordinates of the features are provided.
The file where the features are described.
Compression format for the feature file.
Format for the feature file, currently GFF (v3.0), GTF or BedGraph.
Specifies which type of feature should be extracted from the feature file, if several are available.
Compression format for output file (if file != none).
Tell if only complete features should be extracted or if partial extraction is allowed.
If yes, features will be extracted “as is”. Otherwise, the invert-complement sequence will be returned if it is located on the negative strand.