Source code for galaxy.datatypes.coverage

"""
Coverage datatypes

"""

import logging
import math

from galaxy.datatypes import metadata
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.tabular import Tabular

log = logging.getLogger(__name__)


[docs]class LastzCoverage(Tabular): file_ext = "coverage" MetadataElement(name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter) MetadataElement(name="positionCol", default=2, desc="Position column", param=metadata.ColumnParameter) MetadataElement(name="forwardCol", default=3, desc="Forward or aggregate read column", param=metadata.ColumnParameter) MetadataElement(name="reverseCol", desc="Optional reverse read column", param=metadata.ColumnParameter, optional=True, no_value=0) MetadataElement(name="columns", default=3, desc="Number of columns", readonly=True, visible=False)
[docs] def get_track_resolution(self, dataset, start, end): range = end - start # Determine appropriate resolution to plot ~1000 points resolution = math.ceil(10 ** math.ceil(math.log10(range / 1000))) # Restrict to valid range resolution = min(resolution, 10000) resolution = max(resolution, 1) return resolution