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Add mafcustomtrack datatype and a UCSC external display application which can be used to view this datatype at UCSC.

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This commit is contained in:
Daniel Blankenberg
2010-06-14 15:05:07 -04:00
parent ce24aa2d0a
commit 2603f7efc2
2 changed files with 35 additions and 0 deletions
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datatypes_conf.xml.sample
+3
View File
@@ -77,6 +77,9 @@
<converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/>
<converter file="maf_to_interval_converter.xml" target_datatype="interval"/>
</datatype>
<datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack">
<display file="ucsc/maf_customtrack.xml" />
</datatype>
<datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/>
<datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" />
<datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
lib/galaxy/datatypes/sequence.py
+32
View File
@@ -424,6 +424,38 @@ class Maf( Alignment ):
except:
return False
class MafCustomTrack( data.Text ):
file_ext = "mafcustomtrack"
MetadataElement( name="vp_chromosome", default='chr1', desc="Viewport Chromosome", readonly=True, optional=True, visible=False, no_value='' )
MetadataElement( name="vp_start", default='1', desc="Viewport Start", readonly=True, optional=True, visible=False, no_value='' )
MetadataElement( name="vp_end", default='100', desc="Viewport End", readonly=True, optional=True, visible=False, no_value='' )
def set_meta( self, dataset, overwrite = True, **kwd ):
"""
Parses and sets viewport metadata from MAF file.
"""
max_block_check = 10
chrom = None
forward_strand_start = float( 'inf' )
forward_strand_end = 0
maf_file = open( dataset.file_name )
maf_file.readline() #move past track line
for block in bx.align.maf.Reader( maf_file ):
ref_comp = block.get_component_by_src_start( dataset.metadata.dbkey )
if ref_comp:
ref_chrom = bx.align.maf.src_split( ref_comp.src )[-1]
if chrom is None:
chrom = ref_chrom
if chrom == ref_chrom:
forward_strand_start = min( forward_strand_start, ref_comp.forward_strand_start )
forward_strand_end = max( forward_strand_end, ref_comp.forward_strand_end )
if forward_strand_end > forward_strand_start:
dataset.metadata.vp_chromosome = chrom
dataset.metadata.vp_start = forward_strand_start
dataset.metadata.vp_end = forward_strand_end
class Axt( data.Text ):
"""Class describing an axt alignment"""