BigBed

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

• Reader type: BigBed.Reader
• Writer 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)