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BED

Description

BED is a text-based file format for representing genomic annotations like genes, transcripts, and so on. A BED file has tab-delimited and variable-length fields; the first three fields denoting a genomic interval are mandatory.

This is an example of RNA transcripts:

chr9    68331023    68424451    NM_015110   0   +
chr9    68456943    68486659    NM_001206   0   -

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

Reader type: BED.Reader
Writer type: BED.Writer
Element type: BED.Record

Examples

Here is a common workflow to iterate over all records in a BED file:

# Import the BED module.
using GenomicFeatures

# Open a BED file.
reader = open(BED.Reader, "data.bed")

# Iterate over records.
for record in reader
    # Do something on record (see Accessors section).
    chrom = BED.chrom(record)
    # ...
end

# Finally, close the reader.
close(reader)

If you repeatedly access records within specific ranges, it would be more efficient to construct an IntervalCollection object from a BED reader:

# Create an interval collection in memory.
icol = open(BED.Reader, "data.bed") do reader
    IntervalCollection(reader)
end

# Query overlapping records.
for interval in eachoverlap(icol, Interval("chrX", 40001, 51500))
    # A record is stored in the metadata field of an interval.
    record = metadata(interval)
    # ...
end

API

# GenomicFeatures.BED.Reader — Type.

BED.Reader(input::IO; index=nothing)
BED.Reader(input::AbstractString; index=:auto)

Create a data reader of the BED file format.

The first argument specifies the data source. When it is a filepath that ends with .bgz, it is considered to be block compression file format (BGZF) and the function will try to find a tabix index file (.tbi) and read it if any. See http://www.htslib.org/doc/tabix.html for bgzip and tabix tools.

Arguments

input: data source
index: path to a tabix file