2.1.6 Extract features from the alignment

The ExtractFeature extracts parts of the alignment corresponding to certain features. The features to extract are typically provided via a GFF file.

Synopsis:

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),                  \
    [...]

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.

compression={none|gzip|zip|bzip2}

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

complete={yes|no}

Tell if only complete features should be extracted or if partial extraction is allowed.

ignore_strand={yes|no}

If yes, features will be extracted “as is”. Otherwise, the invert-complement sequence will be returned if it is located on the negative strand.