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Enable visualization of ENCODE peak tracks. Create 'encodepeak' datatype and add data providers for new datatype.

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This commit is contained in:
Jeremy Goecks
2012-02-23 12:23:36 -05:00
parent 214fe94144
commit e5e5cebe6b
6 changed files with 217 additions and 3 deletions
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datatypes_conf.xml.sample
+5
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@@ -130,6 +130,11 @@
<datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack">
<display file="ucsc/maf_customtrack.xml" />
</datatype>
<datatype extension="encodepeak" type="galaxy.datatypes.interval:ENCODEPeak" display_in_upload="True">
<converter file="encodepeak_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
<converter file="encodepeak_to_bgzip_converter.xml" target_datatype="bgzip"/>
<converter file="encodepeak_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
</datatype>
<datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/>
<datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" />
<datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/>
lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
+19
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@@ -0,0 +1,19 @@
<tool id="CONVERTER_encodepeak_to_bgzip_0" name="Convert ENCODEPeak to BGZIP" version="1.0.0" hidden="true">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<command interpreter="python">bgzip.py
-c ${input1.metadata.chromCol}
-s ${input1.metadata.startCol}
-e ${input1.metadata.endCol}
$input1 $output1
</command>
<inputs>
<page>
<param format="ENCODEPeak" name="input1" type="data" label="Choose ENCODEPeak file"/>
</page>
</inputs>
<outputs>
<data format="bgzip" name="output1"/>
</outputs>
<help>
</help>
</tool>
lib/galaxy/datatypes/converters/encodepeak_to_summary_tree_converter.xml
+20
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@@ -0,0 +1,20 @@
<tool id="CONVERTER_encodepeak_to_summary_tree_0" name="Convert ENCODEPeak to Summary Tree" version="1.0.0" hidden="true">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<command interpreter="python">interval_to_summary_tree_converter.py
-c ${input1.metadata.chromCol}
-s ${input1.metadata.startCol}
-e ${input1.metadata.endCol}
$input1 $output1
</command>
<inputs>
<page>
<param format="ENCODEPeak" name="input1" type="data" label="Choose ENCODEPeak file"/>
</page>
</inputs>
<outputs>
<data format="summary_tree" name="output1"/>
</outputs>
<help>
</help>
</tool>
lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
+20
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@@ -0,0 +1,20 @@
<tool id="CONVERTER_encodepeak_to_tabix_0" name="Convert ENCODEPeak to tabix" version="1.0.0" hidden="true">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<command interpreter="python">interval_to_tabix_converter.py
-c ${input1.metadata.chromCol}
-s ${input1.metadata.startCol}
-e ${input1.metadata.endCol}
$input1 $bgzip $output1
</command>
<inputs>
<page>
<param format="encodepeak" name="input1" type="data" label="Choose ENCODEPeak file"/>
<param format="bgzip" name="bgzip" type="data" label="BGZIP file"/>
</page>
</inputs>
<outputs>
<data format="tabix" name="output1"/>
</outputs>
<help>
</help>
</tool>
lib/galaxy/datatypes/interval.py
+30
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@@ -1263,6 +1263,36 @@ class CustomTrack ( Tabular ):
except:
return False
return True
class ENCODEPeak( Interval ):
'''
Human ENCODE peak format. There are both broad and narrow peak formats.
Formats are very similar; narrow peak has an additional column, though.
Broad peak ( http://genome.ucsc.edu/FAQ/FAQformat#format13 ):
This format is used to provide called regions of signal enrichment based
on pooled, normalized (interpreted) data. It is a BED 6+3 format.
Narrow peak http://genome.ucsc.edu/FAQ/FAQformat#format12 and :
This format is used to provide called peaks of signal enrichment based on
pooled, normalized (interpreted) data. It is a BED6+4 format.
'''
file_ext = "encodepeak"
column_names = [ 'Chrom', 'Start', 'End', 'Name', 'Score', 'Strand', 'SignalValue', 'pValue', 'qValue', 'Peak' ]
"""Add metadata elements"""
MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter )
MetadataElement( name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter )
MetadataElement( name="endCol", default=3, desc="End column", param=metadata.ColumnParameter )
MetadataElement( name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0 )
MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False )
def sniff( self, filename ):
return Exception( "Unimplemented Function" )
def get_track_type( self ):
return "FeatureTrack", {"data": "tabix", "index": "summary_tree"}
if __name__ == '__main__':
import doctest, sys
lib/galaxy/visualization/tracks/data_providers.py
+123 -3
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@@ -19,7 +19,7 @@ from galaxy.util.lrucache import LRUCache
from galaxy.visualization.tracks.summary import *
import galaxy_utils.sequence.vcf
from galaxy.datatypes.tabular import Vcf
from galaxy.datatypes.interval import Bed, Gff, Gtf
from galaxy.datatypes.interval import Bed, Gff, Gtf, ENCODEPeak
from pysam import csamtools, ctabix
@@ -288,7 +288,7 @@ class BedDataProvider( TracksDataProvider ):
Provides
"""
# Build data to return. Payload format is:
# [ <guid/offset>, <start>, <end>, <name>, <score>, <strand>, <thick_start>,
# [ <guid/offset>, <start>, <end>, <name>, <strand>, <thick_start>,
# <thick_end>, <blocks> ]
#
# First three entries are mandatory, others are optional.
@@ -965,6 +965,126 @@ class GFFDataProvider( TracksDataProvider ):
return { 'data': results, 'message': message }
#
# -- ENCODE Peak data providers.
#
class ENCODEPeakDataProvider( TracksDataProvider ):
"""
Abstract class that processes ENCODEPeak data from native 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 process_data( self, iterator, start_val=0, max_vals=None, **kwargs ):
"""
Provides
"""
## FIXMEs:
# (1) should be able to unify some of this code with BedDataProvider.process_data
# (2) are optional number of parameters supported?
# Build data to return. Payload format is:
# [ <guid/offset>, <start>, <end>, <name>, <strand>, <thick_start>,
# <thick_end>, <blocks> ]
#
# First three entries are mandatory, others are optional.
#
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
feature = line.split()
length = len( feature )
# Feature initialization.
payload = [
# GUID is just a hash of the line
hash( line ),
# Add start, end.
int( feature[1] ),
int( feature[2] )
]
if no_detail:
rval.append( payload )
continue
# Extend with additional data.
payload.extend( [
# Add name, strand.
feature[3],
feature[5],
# Thick start, end are feature start, end for now.
int( feature[1] ),
int( feature[2] ),
# No blocks.
None,
# Filtering data: Score, signalValue, pValue, qValue.
float( feature[4] ),
float( feature[6] ),
float( feature[7] ),
float( feature[8] )
] )
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 ENCODEPeakTabixDataProvider( TabixDataProvider, ENCODEPeakDataProvider ):
"""
Provides data from an ENCODEPeak dataset indexed via tabix.
"""
def get_filters( self ):
"""
Returns filters for dataset.
"""
# HACK: first 8 fields are for drawing, so start filter column index at 9.
filter_col = 8
filters = []
filters.append( { 'name': 'Score',
'type': 'number',
'index': filter_col,
'tool_id': 'Filter1',
'tool_exp_name': 'c6' } )
filter_col += 1
filters.append( { 'name': 'Signal Value',
'type': 'number',
'index': filter_col,
'tool_id': 'Filter1',
'tool_exp_name': 'c7' } )
filter_col += 1
filters.append( { 'name': 'pValue',
'type': 'number',
'index': filter_col,
'tool_id': 'Filter1',
'tool_exp_name': 'c8' } )
filter_col += 1
filters.append( { 'name': 'qValue',
'type': 'number',
'index': filter_col,
'tool_id': 'Filter1',
'tool_exp_name': 'c9' } )
return filters
#
# -- Helper methods. --
@@ -974,7 +1094,7 @@ class GFFDataProvider( TracksDataProvider ):
# 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: VcfTabixDataProvider, Bed: BedTabixDataProvider, "default" : TabixDataProvider },
"tabix": { Vcf: VcfTabixDataProvider, Bed: BedTabixDataProvider, ENCODEPeak: ENCODEPeakTabixDataProvider, "default" : TabixDataProvider },
"interval_index": IntervalIndexDataProvider,
"bai": BamDataProvider,
"bam": SamDataProvider,