From 97e69fbbdfd820b3044ef3289484850bf3faa566 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 17 Aug 2012 13:55:37 -0400
Subject: [PATCH 1/9] Fix chunk-serving logic for tabular files.

---
 lib/galaxy/datatypes/tabular.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

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=[] )
+

From 3360fe30725e8aeb45595a44936470753d264811 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Fri, 17 Aug 2012 14:39:32 -0400
Subject: [PATCH 2/9] new data for bwa_wrapper/bwa_color_wrapper functional
 tests


From dbc2c27a82c11d6693b92c9dd8358879390cfca8 Mon Sep 17 00:00:00 2001
From: Scott McManus <scottmcmanus@gatech.edu>
Date: Fri, 17 Aug 2012 15:15:48 -0400
Subject: [PATCH 3/9] Minor tweak to exit code handling

---
 lib/galaxy/jobs/__init__.py | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

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

From 860bb2673c6a0324a6d0dc4738fe632d2e1a458b Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 17 Aug 2012 17:49:41 -0400
Subject: [PATCH 4/9] Converters enhancements: (a) ignore track lines in wiggle
 to bigwig converter and add clip option and (b) enable visualization of
 bedgraph datasets via a bedgraph to bigwig converter.

---
 .../converters/bedgraph_to_bigwig_converter.xml    | 14 ++++++++++++++
 .../converters/wig_to_bigwig_converter.xml         |  2 +-
 lib/galaxy/datatypes/interval.py                   |  5 +++--
 3 files changed, 18 insertions(+), 3 deletions(-)
 create mode 100644 lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml

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 @@
+<tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" hidden="true">
+  <!-- Used internally to generate track indexes -->
+  <command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command>
+  <inputs>
+    <page>
+      <param format="bedgraph" name="input" type="data" label="Choose wiggle"/>
+    </page>
+   </inputs>
+   <outputs>
+      <data format="bigwig" name="output"/>
+   </outputs>
+  <help>
+  </help>
+</tool>
\ 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 @@
 <tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" hidden="true">
   <!-- Used internally to generate track indexes -->
-  <command>wigToBigWig $input $chromInfo $output</command>
+  <command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command>
   <inputs>
     <page>
       <param format="wig" name="input" type="data" label="Choose wiggle"/>
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"""

From 5ab62c87460b61c29e22e9bf33bde57e93c719f8 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sat, 18 Aug 2012 18:00:31 -0400
Subject: [PATCH 5/9] Streamline creation of stats for BBI tracks data
 provider.

---
 .../visualization/tracks/data_providers.py    | 37 ++++++++++---------
 1 file changed, 20 insertions(+), 17 deletions(-)

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

From 871f72c9569ff2b409a06ac341162ba8e079f689 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Sun, 19 Aug 2012 15:42:11 -0400
Subject: [PATCH 6/9] Trackster: for explicit coverage histogram mode in
 Feature Tracks, use coverage indices rather than computing on client side.

---
 lib/galaxy/web/controllers/tracks.py |  16 +++-
 static/scripts/viz/trackster.js      | 109 +++------------------------
 2 files changed, 27 insertions(+), 98 deletions(-)

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;
         }

From 009bd6fed69a63e6b2ef3482c56ec59487ae7a07 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 20 Aug 2012 09:57:25 -0400
Subject: [PATCH 7/9] Fix URL generation bug when dictifying tools.

---
 lib/galaxy/tools/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 ) )
             

From 8eea8de39ac593fcd1a03acba6a08c88a89fae2c Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 20 Aug 2012 10:27:44 -0400
Subject: [PATCH 8/9] Make 'add dataset to trackster' dialog compatiable with
 new modal behavior.

---
 templates/root/history.mako | 1 -
 1 file changed, 1 deletion(-)

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();

From 5046dac56331880a92ff36640ace51f662d7ae0c Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Mon, 20 Aug 2012 13:50:12 -0400
Subject: [PATCH 9/9] fix to gff_to_fli.py to avoid breaking unittests

---
 lib/galaxy/datatypes/converters/gff_to_fli.py | 92 ++++++++++---------
 1 file changed, 48 insertions(+), 44 deletions(-)

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