2.2.10 Remove sequences from features from the alignment

The FeatureFilter remove parts of the alignment corresponding to certain features. The features to extract are typically provided via a GFF file. See ExtractFeature in order to keep only the feature parts.

Synopsis:

maf.filter=                                 \
    [...],
    FeatureFilter(                          \
        ref_species=species1,               \
        feature.file=species1.gff3,         \
        feature.file.compression=none,      \
        feature.format=GFF,                 \
        feature.type=(mRNA,tRNA),           \
        file=data.trash_features.maf.gz,    \
        compression=gzip),                  \
    [...]

Arguments:

ref_species={string}

The name of the species for which the coordinates of the features are provided.

feature.file={path}

The file where the features are described.

feature.file.compression={none|gzip|zip|bzip2}

Compression format for the feature file.

feature.format={GFF|GTF|BedGraph}

Format for the feature file, currently GFF (v3.0), GTF or BedGraph.

feature.type={all|(list)}

Specifies which type of feature should be extracted from the feature file, if several are available.

file={none|{path}}

An optional file were extracted features will be stored, in the MAF format.

compression={none|gzip|zip|bzip2}

Compression format for output file (if file != none).