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Viz framework: bigwig fixes and remove unnecessary type casting.

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This commit is contained in:
Jeremy Goecks
2012-07-19 10:59:20 -04:00
parent 5756d21059
commit 6a591eb48b
3 changed files with 27 additions and 22 deletions
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lib/galaxy/visualization/tracks/data_providers.py
+23 -19
View File
@@ -465,8 +465,8 @@ class RawBedDataProvider( BedDataProvider ):
feature_start = int( feature[1] )
feature_end = int( feature[2] )
if ( chrom is not None and feature_chrom != chrom ) \
or ( start is not None and feature_start > int( end ) ) \
or ( end is not None and feature_end < int( start ) ):
or ( start is not None and feature_start > end ) \
or ( end is not None and feature_end < start ):
continue
yield line
return line_filter_iter()
@@ -599,7 +599,7 @@ class RawVcfDataProvider( VcfDataProvider ):
if len( alt ) > longest_alt:
longest_alt = len( alt )
variant_end = variant_start + abs( len( ref ) - longest_alt )
if variant_chrom != chrom or variant_start > int( end ) or variant_end < int( start ):
if variant_chrom != chrom or variant_start > end or variant_end < start:
continue
yield line
return line_filter_iter()
@@ -898,16 +898,16 @@ class BBIDataProvider( TracksDataProvider ):
return all_dat is not None
def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ):
# Bigwig has the possibility of it being a standalone bigwig file, in which case we use
# original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset
# Bigwig can be a standalone bigwig file, in which case we use
# original_dataset, or coming from wig->bigwig conversion in
# which we use converted_dataset
f, bbi = self._get_dataset()
# If the stats kwarg was provide, we compute overall summary data for
# the entire chromosome, but no reduced data -- currently only
# providing values used by trackster to determine the default range
# If the stats kwarg was provide, we compute overall summary data for the
# range defined by start and end but no reduced data. This is currently
# used by client to determine the default range.
if 'stats' in kwargs:
# FIXME: use actual chromosome size
summary = bbi.summarize( chrom, 0, 214783647, 1 )
summary = bbi.summarize( chrom, start, end, 1 )
f.close()
if summary is None:
return None
@@ -927,9 +927,6 @@ class BBIDataProvider( TracksDataProvider ):
return dict( data=dict( min=summary.min_val[0], max=summary.max_val[0], mean=mean, sd=sd ) )
start = int(start)
end = int(end)
# The following seems not to work very well, for example it will only return one
# data point if the tile is 1280px wide. Not sure what the intent is.
@@ -943,13 +940,22 @@ class BBIDataProvider( TracksDataProvider ):
#else:
# num_points = min(num_points, 500)
# For now, we'll do 1000 data points by default However, the summaries
# For now, we'll do 1000 data points by default. However, the summaries
# don't seem to work when a summary pixel corresponds to less than one
# datapoint, so we prevent that.
# FIXME: need to switch over to using the full data at high levels of
# detail.
# FIXME: need to choose the number of points to maximize coverage of the area.
# It appears that BBI calculates points using intervals of
# floor( num_points / end - start )
# In some cases, this prevents sampling near the end of the interval,
# especially when (a) the total interval is small ( < 20-30Kb) and (b) the
# computed interval size has a large fraction, e.g. 14.7 or 35.8
num_points = min( 1000, end - start )
# HACK to address the FIXME above; should generalize.
if end - start <= 2000:
num_points = end - start
summary = bbi.summarize( chrom, start, end, num_points )
f.close()
@@ -958,7 +964,6 @@ class BBIDataProvider( TracksDataProvider ):
if summary:
#mean = summary.sum_data / summary.valid_count
## Standard deviation by bin, not yet used
## var = summary.sum_squares - mean
## var /= minimum( valid_count - 1, 1 )
@@ -968,7 +973,7 @@ class BBIDataProvider( TracksDataProvider ):
step_size = (end - start) / num_points
for i in range( num_points ):
result.append( (pos, float_nan( summary.sum_data[i] ) ) )
result.append( (pos, float_nan( summary.sum_data[i] / summary.valid_count[i] ) ) )
pos += step_size
return { 'data': result }
@@ -1078,7 +1083,6 @@ class RawGFFDataProvider( TracksDataProvider ):
Returns an iterator that provides data in the region chrom:start-end as well as
a file offset.
"""
start, end = int( start ), int( end )
source = open( self.original_dataset.file_name )
def features_in_region_iter():
lib/galaxy/web/controllers/tracks.py
+3 -1
View File
@@ -267,6 +267,8 @@ class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryDat
msg = self.check_dataset_state( trans, dataset )
if msg:
return msg
low, high = int( low ), int( high )
# Return data.
data = None
@@ -402,7 +404,7 @@ class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryDat
data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps )
# Get and return data from data_provider.
result = data_provider.get_data( chrom, low, high, int( start_val ), int( max_vals ), **kwargs )
result = data_provider.get_data( chrom, int( low ), int( high ), int( start_val ), int( max_vals ), **kwargs )
result.update( { 'dataset_type': tracks_dataset_type, 'extra_info': extra_info } )
return result
static/scripts/viz/trackster.js
+1 -2
View File
@@ -4266,9 +4266,8 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
},
predraw_init: function() {
var track = this;
track.vertical_range = undefined;
return $.getJSON( track.data_url, { stats: true, chrom: track.view.chrom, low: null, high: null,
return $.getJSON( track.data_url, { stats: true, chrom: track.view.chrom, low: 0, high: track.view.max_high,
hda_ldda: track.hda_ldda, dataset_id: track.dataset_id }, function(result) {
track.container_div.addClass( "line-track" );
var data = result.data;