diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
new file mode 100644
index 00000000000..77d2c2a42e6
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
@@ -0,0 +1,14 @@
+
+
+ grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/lib/galaxy/datatypes/converters/gff_to_fli.py b/lib/galaxy/datatypes/converters/gff_to_fli.py
index cfa056e573f..ef38576a5a3 100644
--- a/lib/galaxy/datatypes/converters/gff_to_fli.py
+++ b/lib/galaxy/datatypes/converters/gff_to_fli.py
@@ -6,48 +6,52 @@ import sys
from galaxy import eggs
from galaxy.datatypes.util.gff_util import read_unordered_gtf, convert_gff_coords_to_bed
-# Process arguments.
-in_fname = sys.argv[1]
-out_fname = sys.argv[2]
+def main():
+ # Process arguments.
+ in_fname = sys.argv[1]
+ out_fname = sys.argv[2]
+
+ # Create dict of name-location pairings.
+ name_loc_dict = {}
+ for feature in read_unordered_gtf( open( in_fname, 'r' ) ):
+ for name in feature.attributes:
+ val = feature.attributes[ name ]
+ try:
+ float( val )
+ continue
+ except:
+ convert_gff_coords_to_bed( feature )
+ # Value is not a number, so it can be indexed.
+ if val not in name_loc_dict:
+ # Value is not in dictionary.
+ name_loc_dict[ val ] = {
+ 'contig': feature.chrom,
+ 'start': feature.start,
+ 'end': feature.end
+ }
+ else:
+ # Value already in dictionary, so update dictionary.
+ loc = name_loc_dict[ val ]
+ if feature.start < loc[ 'start' ]:
+ loc[ 'start' ] = feature.start
+ if feature.end > loc[ 'end' ]:
+ loc[ 'end' ] = feature.end
+
+ # Print name, loc in sorted order.
+ out = open( out_fname, 'w' )
+ max_len = 0
+ entries = []
+ for name in sorted( name_loc_dict.iterkeys() ):
+ loc = name_loc_dict[ name ]
+ entry = '%s\t%s' % ( name, '%s:%i-%i' % ( loc[ 'contig' ], loc[ 'start' ], loc[ 'end' ] ) )
+ if len( entry ) > max_len:
+ max_len = len( entry )
+ entries.append( entry )
+
+ out.write( str( max_len + 1 ).ljust( max_len ) + '\n' )
+ for entry in entries:
+ out.write( entry.ljust( max_len ) + '\n' )
+ out.close()
-# Create dict of name-location pairings.
-name_loc_dict = {}
-for feature in read_unordered_gtf( open( in_fname, 'r' ) ):
- for name in feature.attributes:
- val = feature.attributes[ name ]
- try:
- float( val )
- continue
- except:
- convert_gff_coords_to_bed( feature )
- # Value is not a number, so it can be indexed.
- if val not in name_loc_dict:
- # Value is not in dictionary.
- name_loc_dict[ val ] = {
- 'contig': feature.chrom,
- 'start': feature.start,
- 'end': feature.end
- }
- else:
- # Value already in dictionary, so update dictionary.
- loc = name_loc_dict[ val ]
- if feature.start < loc[ 'start' ]:
- loc[ 'start' ] = feature.start
- if feature.end > loc[ 'end' ]:
- loc[ 'end' ] = feature.end
-
-# Print name, loc in sorted order.
-out = open( out_fname, 'w' )
-max_len = 0
-entries = []
-for name in sorted( name_loc_dict.iterkeys() ):
- loc = name_loc_dict[ name ]
- entry = '%s\t%s' % ( name, '%s:%i-%i' % ( loc[ 'contig' ], loc[ 'start' ], loc[ 'end' ] ) )
- if len( entry ) > max_len:
- max_len = len( entry )
- entries.append( entry )
-
-out.write( str( max_len + 1 ).ljust( max_len ) + '\n' )
-for entry in entries:
- out.write( entry.ljust( max_len ) + '\n' )
-out.close()
\ No newline at end of file
+if __name__ == '__main__':
+ main()
\ No newline at end of file
diff --git a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
index e85c3a7b138..d90702efe78 100644
--- a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
@@ -1,6 +1,6 @@
- wigToBigWig $input $chromInfo $output
+ grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 69c77a553db..23c81cf48d2 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -338,7 +338,7 @@ class BedGraph( Interval ):
file_ext = "bedgraph"
def get_track_type( self ):
- return "LineTrack", {"data": "array_tree"}
+ return "LineTrack", { "data": "bigwig", "index": "bigwig" }
def as_ucsc_display_file( self, dataset, **kwd ):
"""
@@ -1141,8 +1141,9 @@ class Wiggle( Tabular, _RemoteCallMixin ):
resolution = min( resolution, 100000 )
resolution = max( resolution, 1 )
return resolution
+
def get_track_type( self ):
- return "LineTrack", {"data": "bigwig", "index": "bigwig"}
+ return "LineTrack", { "data": "bigwig", "index": "bigwig" }
class CustomTrack ( Tabular ):
"""UCSC CustomTrack"""
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index ce3b043b658..0939edae159 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -264,10 +264,10 @@ class Tabular( data.Text ):
def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None):
#TODO Prevent failure when displaying extremely long > 50kb lines.
- if to_ext or not preview:
- return self._serve_raw(trans, dataset, to_ext)
if chunk:
return self.get_chunk(trans, dataset, chunk)
+ if to_ext or not preview:
+ return self._serve_raw(trans, dataset, to_ext)
else:
column_names = 'null'
if dataset.metadata.column_names:
@@ -644,4 +644,5 @@ class FeatureLocationIndex( Tabular ):
"""
file_ext='fli'
MetadataElement( name="columns", default=2, desc="Number of columns", readonly=True, visible=False )
- MetadataElement( name="column_types", default=['str', 'str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False, no_value=[] )
\ No newline at end of file
+ MetadataElement( name="column_types", default=['str', 'str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False, no_value=[] )
+
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 5ac63f9957b..50c185834c2 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -490,7 +490,6 @@ class JobWrapper( object ):
if stderr contains anything, then False is returned.
Note that the job id is just for messages.
"""
- err_msg = ""
# By default, the tool succeeded. This covers the case where the code
# has a bug but the tool was ok, and it lets a workflow continue.
success = True
@@ -507,7 +506,7 @@ class JobWrapper( object ):
# Check the exit code ranges in the order in which
# they were specified. Each exit_code is a StdioExitCode
# that includes an applicable range. If the exit code was in
- # that range, then apply the error level and add in a message.
+ # that range, then apply the error level and add a message.
# If we've reached a fatal error rule, then stop.
max_error_level = galaxy.tools.StdioErrorLevel.NO_ERROR
for stdio_exit_code in self.tool.stdio_exit_codes:
@@ -515,20 +514,16 @@ class JobWrapper( object ):
tool_exit_code <= stdio_exit_code.range_end ):
# Tack on a generic description of the code
# plus a specific code description. For example,
- # this might append "Job 42: Warning: Out of Memory\n".
- # TODO: Find somewhere to stick the err_msg -
- # possibly to the source (stderr/stdout), possibly
- # in a new db column.
+ # this might prepend "Job 42: Warning: Out of Memory\n".
code_desc = stdio_exit_code.desc
if ( None == code_desc ):
code_desc = ""
- tool_msg = ( "Job %s: %s: Exit code %d: %s" % (
- job.get_id_tag(),
- galaxy.tools.StdioErrorLevel.desc( tool_exit_code ),
+ tool_msg = ( "%s: Exit code %d: %s" % (
+ galaxy.tools.StdioErrorLevel.desc( stdio_exit_code.error_level ),
tool_exit_code,
code_desc ) )
- log.info( tool_msg )
- stderr = err_msg + stderr
+ log.info( "Job %s: %s" % (job.get_id_tag(), tool_msg) )
+ stderr = tool_msg + "\n" + stderr
max_error_level = max( max_error_level,
stdio_exit_code.error_level )
if ( max_error_level >=
@@ -571,7 +566,6 @@ class JobWrapper( object ):
re.IGNORECASE )
if ( regex_match ):
rexmsg = self.regex_err_msg( regex_match, regex)
- # DELETEME
log.info( "Job %s: %s"
% ( job.get_id_tag(), rexmsg ) )
stderr = rexmsg + "\n" + stderr
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index b829f86f5a2..f686a9216a9 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2631,7 +2631,7 @@ class Tool:
if for_link:
# Create tool link.
if not self.tool_type.startswith( 'data_source' ):
- link = url_for( controller='tool_runner', tool_id=self.id )
+ link = url_for( '/tool_runner', tool_id=self.id )
else:
link = url_for( self.action, **self.get_static_param_values( trans ) )
diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index 0999f9e3932..64363b4dac6 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -968,29 +968,32 @@ class BBIDataProvider( TracksDataProvider ):
# which we use converted_dataset
f, bbi = self._get_dataset()
- # 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 requested, compute overall summary data for the range
+ # start:endbut no reduced data. This is currently used by client
+ # to determine the default range.
if 'stats' in kwargs:
summary = bbi.summarize( chrom, start, end, 1 )
f.close()
- if summary is None:
- return None
- else:
+
+ min = 0
+ max = 0
+ mean = 0
+ sd = 0
+ if summary is not None:
# Does the summary contain any defined values?
valid_count = summary.valid_count[0]
- if summary.valid_count < 1:
- return None
+ if summary.valid_count > 0:
+ # Compute $\mu \pm 2\sigma$ to provide an estimate for upper and lower
+ # bounds that contain ~95% of the data.
+ mean = summary.sum_data[0] / valid_count
+ var = summary.sum_squares[0] - mean
+ if valid_count > 1:
+ var /= valid_count - 1
+ sd = numpy.sqrt( var )
+ min = summary.min_val[0]
+ max = summary.max_val[0]
- # Compute $\mu \pm 2\sigma$ to provide an estimate for upper and lower
- # bounds that contain ~95% of the data.
- mean = summary.sum_data[0] / valid_count
- var = summary.sum_squares[0] - mean
- if valid_count > 1:
- var /= valid_count - 1
- sd = numpy.sqrt( var )
-
- return dict( data=dict( min=summary.min_val[0], max=summary.max_val[0], mean=mean, sd=sd ) )
+ return dict( data=dict( min=min, max=max, mean=mean, sd=sd ) )
# Sample from region using approximately this many samples.
N = 1000
diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py
index d468b0dfb35..8c21cd7f8ba 100644
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -387,7 +387,21 @@ class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryDat
return return_message
extra_info = None
- if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and kwargs.get("mode", "Auto") == "Auto":
+ mode = kwargs.get( "mode", "Auto" )
+ # Handle histogram mode uniquely for now:
+ if mode == "Coverage":
+ # Get summary using minimal cutoffs.
+ tracks_dataset_type = data_sources['index']['name']
+ converted_dataset = dataset.get_converted_dataset( trans, tracks_dataset_type )
+ indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset )
+ summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], detail_cutoff=0, draw_cutoff=0 )
+ if summary == "detail":
+ # Use maximum level of detail--2--to get summary data no matter the resolution.
+ summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], level=2, detail_cutoff=0, draw_cutoff=0 )
+ frequencies, max_v, avg_v, delta = summary
+ return { 'dataset_type': tracks_dataset_type, 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta }
+
+ if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and mode == "Auto":
# Only check for summary_tree if it's Auto mode (which is the default)
#
# Have to choose between indexer and data provider
diff --git a/static/scripts/viz/trackster.js b/static/scripts/viz/trackster.js
index 7f8acacc6d0..645b00b2be0 100644
--- a/static/scripts/viz/trackster.js
+++ b/static/scripts/viz/trackster.js
@@ -4433,7 +4433,7 @@ var FeatureTrack = function(view, container, obj_dict) {
// initialization code.
//
var track = this;
- this.display_modes = ["Auto", "Histogram", "Dense", "Squish", "Pack"];
+ this.display_modes = ["Auto", "Coverage", "Dense", "Squish", "Pack"];
//
// Initialization.
@@ -4516,8 +4516,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
var track = this,
i;
- // If mode is Histogram and tiles do not share max, redraw tiles as necessary using new max.
- if (track.mode === "Histogram") {
+ // If mode is Coverage and tiles do not share max, redraw tiles as necessary using new max.
+ if (track.mode === "Coverage") {
// Get global max.
var global_max = -1;
for (i = 0; i < tiles.length; i++) {
@@ -4534,7 +4534,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
track.draw_helper(true, width, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { more_tile_data: { max: global_max } } );
}
}
- }
+ }
//
// Update filter attributes, UI.
@@ -4649,86 +4649,6 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
return slotter.slot_features( features );
},
- /**
- * Given feature data, returns summary tree data. Feature data must be sorted by start
- * position. Return value is a dict with keys 'data', 'delta' (bin size) and 'max.' Data
- * is a two-item list; first item is bin start, second is bin's count.
- */
- get_summary_tree_data: function(data, low, high, num_bins) {
- if (num_bins > high - low) {
- num_bins = high - low;
- }
- var bin_size = Math.floor((high - low)/num_bins),
- bins = [],
- max_count = 0;
-
- /*
- // For debugging:
- for (var i = 0; i < data.length; i++)
- console.log("\t", data[i][1], data[i][2], data[i][3]);
- */
-
- //
- // Loop through bins, counting data for each interval.
- //
- var data_index_start = 0,
- data_index = 0,
- data_interval,
- bin_index = 0,
- bin_interval = [],
- cur_bin;
-
- // Set bin interval.
- var set_bin_interval = function(interval, low, bin_index, bin_size) {
- interval[0] = low + bin_index * bin_size;
- interval[1] = low + (bin_index + 1) * bin_size;
- };
-
- // Loop through bins, data to compute bin counts. Only compute bin counts as long
- // as there is data.
- while (bin_index < num_bins && data_index_start !== data.length) {
- // Find next bin that has data.
- var bin_has_data = false;
- for (; bin_index < num_bins && !bin_has_data; bin_index++) {
- set_bin_interval(bin_interval, low, bin_index, bin_size);
- // Loop through data and break if data found that goes in bin.
- for (data_index = data_index_start; data_index < data.length; data_index++) {
- data_interval = data[data_index].slice(1, 3);
- if (is_overlap(data_interval, bin_interval)) {
- bin_has_data = true;
- break;
- }
- }
- // Break from bin loop if this bin has data.
- if (bin_has_data) {
- break;
- }
- }
-
- // Set start index to current data, which is the first to overlap with this bin
- // and perhaps with later bins.
- data_start_index = data_index;
-
- // Count intervals that overlap with bin.
- bins[bins.length] = cur_bin = [bin_interval[0], 0];
- for (; data_index < data.length; data_index++) {
- data_interval = data[data_index].slice(1, 3);
- if (is_overlap(data_interval, bin_interval)) {
- cur_bin[1]++;
- }
- else { break; }
- }
-
- // Update max count.
- if (cur_bin[1] > max_count) {
- max_count = cur_bin[1];
- }
-
- // Go to next bin.
- bin_index++;
- }
- return {max: max_count, delta: bin_size, data: bins};
- },
/**
* Returns appropriate display mode based on data.
*/
@@ -4766,8 +4686,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
* number of pixels required.
*/
get_canvas_height: function(result, mode, w_scale, canvas_width) {
- if (mode === "summary_tree" || mode === "Histogram") {
- // Extra padding at top of summary tree so label does not overlap data.
+ if (mode === "summary_tree" || mode === "Coverage") {
return this.summary_draw_height;
}
else {
@@ -4796,16 +4715,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
tile_high = region.get('end'),
left_offset = this.left_offset;
- // Drawing the summary tree (feature coverage histogram)
- if (mode === "summary_tree" || mode === "Histogram") {
- // Get summary tree data if necessary and set max if there is one.
- if (result.dataset_type !== "summary_tree") {
- var st_data = this.get_summary_tree_data(result.data, tile_low, tile_high, 200);
- if (result.max) {
- st_data.max = result.max;
- }
- result = st_data;
- }
+ // Drawing the summary tree.
+ if (mode === "summary_tree" || mode === "Coverage") {
// Paint summary tree into canvas
var painter = new painters.SummaryTreePainter(result, tile_low, tile_high, this.prefs);
painter.draw(ctx, canvas.width, canvas.height, w_scale);
@@ -4872,7 +4783,11 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
if (mode === "Auto") {
return true;
}
- // All other modes--Histogram, Dense, Squish, Pack--require data + details.
+ // Histogram mode requires summary_tree data.
+ else if (mode === "Coverage") {
+ return data.dataset_type === "summary_tree";
+ }
+ // All other modes--Dense, Squish, Pack--require data + details.
else if (data.extra_info === "no_detail" || data.dataset_type === "summary_tree") {
return false;
}
diff --git a/templates/root/history.mako b/templates/root/history.mako
index ad9da4d6157..5dcfdc768d7 100644
--- a/templates/root/history.mako
+++ b/templates/root/history.mako
@@ -250,7 +250,6 @@ $(function() {
},
"View in saved visualization": function() {
// Show new modal with saved visualizations.
- parent.hide_modal();
parent.show_modal("Add Data to Saved Visualization", table_html, {
"Cancel": function() {
parent.hide_modal();