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bigBed

Description

bigBed is a binary file format for representing genomic annotations and often created from BED files. bigBed files are indexed to quickly fetch specific regions.

I/O tools for bigBed are provided from the GenomicFeatures.BigBed module, which exports following three types:

  • Reader type: BigBed.Reader
  • Writre type: BigBed.Writer
  • Element type: BigBed.Record

Examples

A common workflow is to open a file, iterate over records, and close the file:

# Import the BigBed module.
using GenomicFeatures

# Open a bigBed file.
reader = open(BigBed.Reader, "data.bb")

# Iterate over records overlapping with a query interval.
for record in eachoverlap(reader, Interval("Chr2", 5001, 6000))
    # Extract the start position, end position and value of the record,
    startpos = BigBed.chromstart(record)
    endpos = BigBed.chromend(record)
    value = BigBed.value(record)
    # and do something...
end

# Finally, close the reader.
close(reader)

Iterating over all records is also supported:

reader = open(BigBed.Reader, "data.bb")
for record in reader
    # ...
end
close(reader)

Creating a bigBed file can be done as follows. The write call takes a tuple of 3-12 elements (i.e. chromosome name, start position, end position, name, score, strand, thickstart, thickend, RGB color, blockcount, blocksizes and blockstarts). The first three are mandatory fields but others are optional.

# Import RGB type.
using ColorTypes
file = open("data.bb", "w")
writer = BigBed.Writer(file, [("chr1", 1000)])
write(writer, ("chr1", 1, 100, "some name", 100, '+', 10, 90, RGB(0.5, 0.1, 0.2), 2, [4, 10], [10, 20]))
close(writer)

API

GenomicFeatures.BigBed.Writer — Type
BigBed.Writer(output::IO, chromlist; binsize=64)

Create a data writer of the bigBed file format.

Arguments

  • output: data sink
  • chromlist: chromosome list with length
  • binsize=64: size of a zoom with the highest resolution

Examples

output = open("data.bb", "w")
writer = BigBed.Writer(output, [("chr1", 12345), ("chr2", 9100)])
write(writer, ("chr1", 101, 150, "gene 1"))
write(writer, ("chr2", 211, 250, "gene 2"))
close(writer)
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