object NcbiRefSeqGffSource

Companion object for NcbiRefSeqGffSource which provides factory methods for parsing RefSeq GFF files. The resulting data is returned as instances of GeneAnnotations.Gene and related classes.

The following link points to a file of the appropriate format that is parsed by this code: https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Macaca_fascicularis/latest_assembly_versions/GCF_000364345.1_Macaca_fascicularis_5.0/GCF_000364345.1_Macaca_fascicularis_5.0_genomic.gff.gz

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  4. def apply(path: FgBioDef.FilePath, includeXs: Boolean, dict: SequenceDictionary): NcbiRefSeqGffSource

    Parses a RefSeq GFF file from an (optionally gzipped) text file.

    Parses a RefSeq GFF file from an (optionally gzipped) text file.

    path

    the path to the file to parse

    includeXs

    whether to include experimental transcripts (i.e. XM_* XP_* and XR_*).

    dict

    a sequence dictionary used to help resolve accessions used in the GFF

    returns

    an instance of NcbiRefSeqGffSource that can be queried for contents

  5. def apply(lines: Iterable[String], includeXs: Boolean, dict: SequenceDictionary): NcbiRefSeqGffSource

    Parses a RefSeq GFF file from a collection of lines of text.

    Parses a RefSeq GFF file from a collection of lines of text.

    lines

    the lines to parse

    includeXs

    whether to include experimental transcripts (i.e. XM_* XP_* and XR_*).

    dict

    a sequence dictionary used to help resolve accessions used in the GFF

    returns

    an instance of NcbiRefSeqGffSource that can be queried for contents

  6. def apply(lines: Iterator[String], includeXs: Boolean, dict: SequenceDictionary): NcbiRefSeqGffSource

    Parses a RefSeq GFF file from an iterator of lines of text.

    Parses a RefSeq GFF file from an iterator of lines of text.

    lines

    the lines to parse

    includeXs

    whether to include experimental transcripts (i.e. XM_* XP_* and XR_*).

    dict

    a sequence dictionary used to help resolve accessions used in the GFF

    returns

    an instance of NcbiRefSeqGffSource that can be queried for contents

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