plastid.readers.wiggle module¶
A single reader for fixedStep wiggle, variableStep wiggle, and bedGraph files.
WiggleReader
is seldom called directly. Typically it is internally called by
GenomeArray
and SparseGenomeArray
, when their
add_from_wiggle()
methods
are called.
See also¶
- UCSC file format FAQ
UCSC Wiggle and bedGraph file specification
GenomeArray
andSparseGenomeArray
Array-like objects that store and index quantitative data over genomes
- class plastid.readers.wiggle.WiggleReader(fh)[source]¶
Bases:
object
Read wiggle and bedGraph files line-by-line, returning tuples of (chromosome, start position, stop position, value). Tuple coordinates are zero-indexed and half-open, regardless of whether the file is a wiggle or bedGraph.
See the UCSC file format FAQ for details.
Methods
next
()Yield a tuple of (chromosome, start, stop, value) for each data line.
- next()[source]¶
Yield a tuple of (chromosome, start, stop, value) for each data line. Header lines are processed internally and not exposed to the user.
All coordinates are returned as 0-based, half-open intervals, following Python conventions.
- Returns
- str
chromosome name
- int
start position, 0-indexed
- int
end position, 0-indexed, half-open
- float
value on chromosome between start and end