root/galaxy-central/lib/galaxy/datatypes/coverage.py

"""
Coverage datatypes

"""
import pkg_resources
pkg_resources.require( "bx-python" )

import logging, os, sys, time, tempfile, shutil
import data
from galaxy import util
from galaxy.datatypes.sniff import *
from galaxy.web import url_for
from cgi import escape
import urllib
from bx.intervals.io import *
from galaxy.datatypes import metadata
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.tabular import Tabular
import math

log = logging.getLogger(__name__)

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 )

    def get_track_window(self, dataset, data, start, end):
        """
        Assumes we have a numpy file.
        """
        # Maybe if we import here people will still be able to use Galaxy when numpy kills it
        pkg_resources.require("numpy>=1.2.1")
        #from numpy.lib import format
        import numpy

        range = end - start
        # Determine appropriate resolution to plot ~1000 points
        resolution = ( 10 ** math.ceil( math.log10( range / 1000 ) ) )
        # Restrict to valid range
        resolution = min( resolution, 10000 )
        resolution = max( resolution, 1 )
        # Memory map the array (don't load all the data)
        data = numpy.load( data )
        # Grab just what we need
        t_start = math.floor( start / resolution )
        t_end = math.ceil( end / resolution )
        x = numpy.arange( t_start, t_end ) * resolution
        y = data[ t_start : t_end ]
    
        return zip(x.tolist(), y.tolist())

    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