1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/af6ed2f06f35/ changeset: af6ed2f06f35 user: jgoecks date: 2011-09-19 17:59:09 summary: Trackster: enable tools that produce BED output to be used in visual analytics framework. Enable cluster tool in Trackster. affected #: 3 files (-1 bytes)

--- a/lib/galaxy/visualization/tracks/data_providers.py Mon Sep 19 10:24:11 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Mon Sep 19 11:59:09 2011 -0400 @@ -135,6 +135,88 @@ { 'name' : attrs[ 'name' ], 'type' : column_types[viz_col_index], \ 'index' : attrs[ 'index' ] } ) return filters + +class BedDataProvider( TracksDataProvider ): + """ + Abstract class that processes BED data from text format to payload format. + + Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] + """ + + def get_iterator( self, chrom, start, end ): + raise "Unimplemented Method" + + def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): + iterator = self.get_iterator( chrom, start, end ) + return self.process_data( iterator, start_val, max_vals, **kwargs ) + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + """ + Provides + """ + # Build data to return. Payload format is: + # [ <guid/offset>, <start>, <end>, <name>, <score>, <strand>, <thick_start>, + # <thick_end>, <blocks> ] + # + # First three entries are mandatory, others are optional. + # + filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) + no_detail = ( "no_detail" in kwargs ) + rval = [] + message = None + for count, line in enumerate( iterator ): + if count < start_val: + continue + if max_vals and count-start_val >= max_vals: + message = ERROR_MAX_VALS % ( max_vals, "features" ) + break + # TODO: can we use column metadata to fill out payload? + # TODO: use function to set payload data + + feature = line.split() + length = len(feature) + # Unique id is just a hash of the line + payload = [ hash(line), int(feature[1]), int(feature[2]) ] + + if no_detail: + rval.append( payload ) + continue + + # Simpler way to add stuff, but type casting is not done. + # Name, score, strand, thick start, thick end. + #end = min( len( feature ), 8 ) + #payload.extend( feature[ 3:end ] ) + + # Name, strand, thick start, thick end. + if length >= 4: + payload.append(feature[3]) + if length >= 6: + payload.append(feature[5]) + if length >= 8: + payload.append(int(feature[6])) + payload.append(int(feature[7])) + + # Blocks. + if length >= 12: + block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] + block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] + blocks = zip( block_sizes, block_starts ) + payload.append( [ ( int(feature[1]) + block[1], int(feature[1]) + block[1] + block[0] ) for block in blocks ] ) + + # Score (filter data) + if length >= 5 and filter_cols and filter_cols[0] == "Score": + payload.append( float(feature[4]) ) + + rval.append( payload ) + + return { 'data': rval, 'message': message } + + def write_data_to_file( self, chrom, start, end, filename ): + iterator = self.get_iterator( chrom, start, end ) + out = open( filename, "w" ) + for line in iterator: + out.write( "%s\n" % line ) + out.close()

class SummaryTreeDataProvider( TracksDataProvider ): """ @@ -573,78 +655,7 @@ results.append( payload )

return { 'data': results, 'message': message } - -class BedDataProvider( TabixDataProvider ): - """ - Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] - """ - - def process_data( self, iterator, start_val=0, max_vals=sys.maxint, **kwargs ): - # - # Build data to return. Payload format is: - # [ <guid/offset>, <start>, <end>, <name>, <score>, <strand>, <thick_start>, - # <thick_end>, <blocks> ] - # - # First three entries are mandatory, others are optional. - # - filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) - no_detail = ( "no_detail" in kwargs ) - rval = [] - message = None - for count, line in enumerate( iterator ): - if count < start_val: - continue - if count-start_val >= max_vals: - message = ERROR_MAX_VALS % ( max_vals, "features" ) - break - # TODO: can we use column metadata to fill out payload? - # TODO: use function to set payload data - - feature = line.split() - length = len(feature) - # Unique id is just a hash of the line - payload = [ hash(line), int(feature[1]), int(feature[2]) ] - - if no_detail: - rval.append( payload ) - continue - - # Simpler way to add stuff, but type casting is not done. - # Name, score, strand, thick start, thick end. - #end = min( len( feature ), 8 ) - #payload.extend( feature[ 3:end ] ) - - # Name, strand, thick start, thick end. - if length >= 4: - payload.append(feature[3]) - if length >= 6: - payload.append(feature[5]) - if length >= 8: - payload.append(int(feature[6])) - payload.append(int(feature[7])) - - # Blocks. - if length >= 12: - block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] - block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] - blocks = zip( block_sizes, block_starts ) - payload.append( [ ( int(feature[1]) + block[1], int(feature[1]) + block[1] + block[0] ) for block in blocks ] ) - - # Score (filter data) - if length >= 5 and filter_cols and filter_cols[0] == "Score": - payload.append( float(feature[4]) )

- rval.append( payload ) - - return { 'data': rval, 'message': message } - - def write_data_to_file( self, chrom, start, end, filename ): - iterator = self.get_iterator( chrom, start, end ) - out = open( filename, "w" ) - for line in iterator: - out.write( "%s\n" % line ) - out.close() - class VcfDataProvider( TabixDataProvider ): """ VCF data provider for the Galaxy track browser. @@ -685,7 +696,7 @@ Provide data from GFF file.

NOTE: this data provider does not use indices, and hence will be very slow - for large datasets. + for large datasets. """ def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ): start, end = int( start ), int( end ) @@ -710,6 +721,30 @@ offset += feature.raw_size

return { 'data': results, 'message': message } + +class BedTabixDataProvider( TabixDataProvider, BedDataProvider ): + """ + Provides data from a BED file indexed via tabix. + """ + pass + +class RawBedDataProvider( BedDataProvider ): + """ + Provide data from BED file. + + NOTE: this data provider does not use indices, and hence will be very slow + for large datasets. + """ + + def get_iterator( self, chrom, start, end ): + def line_filter_iter(): + for line in open( self.original_dataset.file_name ): + feature = line.split() + feature_chrom, feature_start, feature_end = feature[ 0:3 ] + if feature_chrom != chrom or feature_start > end or feature_end < start: + continue + yield line + return line_filter_iter()

# # Helper methods. @@ -719,7 +754,7 @@ # type. First key is converted dataset type; if result is another dict, second key # is original dataset type. TODO: This needs to be more flexible. dataset_type_name_to_data_provider = { - "tabix": { Vcf: VcfDataProvider, Bed: BedDataProvider, "default" : TabixDataProvider }, + "tabix": { Vcf: VcfDataProvider, Bed: BedTabixDataProvider, "default" : TabixDataProvider }, "interval_index": IntervalIndexDataProvider, "bai": BamDataProvider, "summary_tree": SummaryTreeDataProvider,

--- a/lib/galaxy/web/controllers/tracks.py Mon Sep 19 10:24:11 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Mon Sep 19 11:59:09 2011 -0400 @@ -397,7 +397,7 @@ def raw_data( self, trans, dataset_id, chrom, low, high, **kwargs ): """ Uses original (raw) dataset to return data. This method is useful - when the dataset is not yet indexed and hence using /data would + when the dataset is not yet indexed and hence using data would be slow because indexes need to be created. """

@@ -409,10 +409,15 @@

# Return data. data = None + # TODO: for raw data requests, map dataset type to provider using dict in data_providers.py if isinstance( dataset.datatype, Gff ): data = GFFDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) data[ 'dataset_type' ] = 'interval_index' data[ 'extra_info' ] = None + if isinstance( dataset.datatype, Bed ): + data = RawBedDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) + data[ 'dataset_type' ] = 'interval_index' + data[ 'extra_info' ] = None return data

@web.json

--- a/tools/new_operations/cluster.xml Mon Sep 19 10:24:11 2011 -0400 +++ b/tools/new_operations/cluster.xml Mon Sep 19 11:59:09 2011 -0400 @@ -1,5 +1,6 @@ <tool id="gops_cluster_1" name="Cluster"><description>the intervals of a dataset</description> + <trackster_conf/><command interpreter="python">gops_cluster.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -d $distance -m $minregions -o $returntype</command><inputs><param format="interval" name="input1" type="data">

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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