I/O
Input
Annotation files are read with GenBank.Reader
and GFF.Reader
. Currently these assume that the file follows either standard GenBank format, or GFF3. Any metadata in GFF3 files, apart from the header, is ignored.
open(GenBank.Reader, "example.gbk") do reader
for record in reader
do_something()
end
end
readgbk(input)
and readgff(input)
are aliases for collect(open(GenBank.Reader, input))
and collect(open(GFF.Reader, input))
, respectively.
GenomicAnnotations.GenBank.Reader
— TypeGenBank.Reader(input::IO)
Create a data reader of the GenBank file format.
GenomicAnnotations.GFF.Reader
— TypeGFF.Reader(input::IO)
Create a data reader of the GFF3 file format.
Output
Annotations can be printed with GenBank formatting using GenBank.Writer
, and as GFF3 with GFF.Writer
. Headers are not automatically converted between formats; GFF.Writer
only prints the header of the first Record
, and only if it starts with a #
, while GenBank.Writer
prints a default header if the stored one starts with #
.
GenomicAnnotations.GenBank.Writer
— TypeGenBank.Writer(output::IO; width=70)
Create a data writer of the GenBank file format.
open(GenBank.Writer, outfile) do writer
write(writer, genome)
end
GenomicAnnotations.GFF.Writer
— TypeGFF.Writer(output::IO; width=70)
Create a data writer of the GFF file format.
open(GFF.Writer, outfile) do writer
write(writer, genome)
end
In the REPL, instances of Gene
are displayed as they would be in the annotation file.