# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks jeremy.goecks@emory.edu # Date 1278981206 14400 # Node ID 7084aafd2e1a77200935a15b64774b0f65ca06f5 # Parent 67392693199489978700ecd35ec463d1901ffe1e Enable bedgraph files to be displayed in UCSC genome browser.
--- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -332,6 +332,56 @@ class BedGraph( Interval ):
def get_track_type( self ): return "LineTrack", {"data": "array_tree"} + + def as_ucsc_display_file( self, dataset, **kwd ): + """ + Returns file contents as is with no modifications. + TODO: this is a functional stub and will need to be enhanced moving forward to provide additional support for bedgraph. + """ + return open( dataset.file_name ) + + def get_estimated_display_viewport( self, dataset ): + """ + Set viewport based on dataset's first 100 lines. + """ + if dataset.has_data() and dataset.state == dataset.states.OK: + try: + # Set seqid, start, stop. + seqid = None + start = 2147483647 # Maximum value of a signed 32 bit integer ( 2**31 - 1 ) + stop = 0 + for i, line in enumerate( file( dataset.file_name ) ): + line = line.rstrip( '\r\n' ) + if not line: + continue + elts = line.split('\t') + if len( elts ) == 4: + # Update seq id, start, end. + if not seqid: + # We can only set the viewport for a single chromosome + seqid = elems[0] + if seqid == elems[0]: + # Make sure we have not spanned chromosomes + start = min( start, int( elems[1] ) ) + stop = max( stop, int( elems[2] ) ) + else: + # We've spanned a chromosome + break + else: + continue + # Only look through 100 lines. + if i > 100: + break + + # Set valid values for start, stop if necessary. + if start == 2147483647: + start = 0 + if stop == 0: + stop = 1 + return ( seqid, str( start ), str( stop ) ) + except: + return( '', '', '' ) + return( '', '', '' )
class Bed( Interval ): """Tab delimited data in BED format"""