# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg dan@bx.psu.edu # Date 1279901436 14400 # Node ID f94f1f2fa4be20f8f90ffa9482a754f69256f449 # Parent cecc290755014c02aa21906d433a3d39f2d657d5 Fixes for generating viewports.

Now, a maximum of 1MB is read from a line to determine the viewport; if a line greater than 10MB is encountered, then no viewport will be generated.

Additional fixes for certain cases when viewport was not determined properly for for WIG tracks and GFF.

--- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -38,6 +38,10 @@ for key, value in alias_spec.items(): for elem in value: alias_helper[elem] = key

+#Constants for configuring viewport generation +VIEWPORT_READLINE_BUFFER_SIZE = 1048576 #1MB +VIEWPORT_MAX_READS_PER_LINE = 10 # If a line is greater than VIEWPORT_MAX_READS_PER_LINE * VIEWPORT_READLINE_BUFFER_SIZE bytes in size, then we will not generate a viewport for that dataset + class Interval( Tabular ): """Tab delimited data containing interval information""" file_ext = "interval" @@ -146,33 +150,55 @@ class Interval( Tabular ): and dataset.metadata.endCol except: return False - def get_estimated_display_viewport( self, dataset ): + def get_estimated_display_viewport( self, dataset, chrom_col = None, start_col = None, end_col = None ): """Return a chrom, start, stop tuple for viewing a file.""" + viewport_feature_count = 100 # viewport should check at least 100 features; excludes comment lines + max_line_count = max( viewport_feature_count, 500 ) # maximum number of lines to check; includes comment lines if self.displayable( dataset ): try: - c, s, e = dataset.metadata.chromCol, dataset.metadata.startCol, dataset.metadata.endCol - c, s, e = int(c)-1, int(s)-1, int(e)-1 - try: - skipme = int(dataset.metadata.comment_lines) - except: - skipme = 0 - peek = [] - for idx, line in enumerate(file(dataset.file_name)): - if line[0] != '#': - peek.append( line.rstrip( '\n\r' ).split() ) - if idx > 100 and idx > skipme: # viewport should have at least 100 features - break - chr, start, stop = peek[skipme][c], int( peek[skipme][s] ), int( peek[skipme][e] ) - for p in peek[(skipme+1):]: - if p[0] == chr: - start = min( start, int( p[s] ) ) - stop = max( stop, int( p[e] ) ) - except Exception, exc: - log.exception( str(exc) ) - return ( None, None, None ) - return (chr, str( start ), str( stop )) - else: - return ( None, None, None ) + chrom = None + start = sys.maxint + end = 0 + if chrom_col is None: + chrom_col = int( dataset.metadata.chromCol ) - 1 + if start_col is None: + start_col = int( dataset.metadata.startCol ) - 1 + if end_col is None: + end_col = int( dataset.metadata.endCol ) - 1 + max_col = max( chrom_col, start_col, end_col ) + fh = open( dataset.file_name ) + while True: + line = fh.readline( VIEWPORT_READLINE_BUFFER_SIZE ) + if not line: break #EOF + if not line.startswith( '#' ): + try: + fields = line.rstrip().split( '\t' ) + if len( fields ) > max_col: + if chrom is None or chrom == fields[ chrom_col ]: + start = min( start, int( fields[ start_col ] ) ) + end = max( end, int( fields[ end_col ] ) ) + chrom = fields[ chrom_col ] #set chrom last, in case start and end are not integers + viewport_feature_count -= 1 + except Exception: + #most likely a non-integer field has been encountered for start / stop + continue + #make sure we are at the next new line + readline_count = VIEWPORT_MAX_READS_PER_LINE + while line.rstrip( '\n\r' ) == line: + assert readline_count > 0, Exception( 'Viewport readline count exceeded for dataset %s.' % dataset.id ) + line = fh.readline( VIEWPORT_READLINE_BUFFER_SIZE ) + if not line: break #EOF + readline_count -= 1 + max_line_count -= 1 + if not viewport_feature_count or not max_line_count: + #exceeded viewport or total line count to check + break + if chrom is not None: + return ( chrom, str( start ), str( end ) ) #Necessary to return strings? + except Exception, e: + #unexpected error, possibly missing metadata + log.exception( str( e ) ) + return ( None, None, None ) #could not determine viewport def as_ucsc_display_file( self, dataset, **kwd ): """Returns file contents with only the bed data""" fd, temp_name = tempfile.mkstemp() @@ -336,49 +362,11 @@ class BedGraph( Interval ): """ return open( dataset.file_name )

- def get_estimated_display_viewport( self, dataset ): + def get_estimated_display_viewport( self, dataset, chrom_col = 0, start_col = 1, end_col = 2 ): """ Set viewport based on dataset's first 100 lines. """ - if self.displayable( dataset ): - 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 - elems = line.split('\t') - if len( elems ) == 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 Exception, exc: - log.exception( str( exc ) ) - return ( None, None, None ) - return ( None, None, None ) + return Interval.get_estimated_display_viewport( self, dataset, chrom_col = chrom_col, start_col = start_col, end_col = end_col )

class Bed( Interval ): """Tab delimited data in BED format""" @@ -644,61 +632,75 @@ class Gff( Tabular, _RemoteCallMixin ): Return a chrom, start, stop tuple for viewing a file. There are slight differences between gff 2 and gff 3 formats. This function should correctly handle both... """ + viewport_feature_count = 100 # viewport should check at least 100 features; excludes comment lines + max_line_count = max( viewport_feature_count, 500 ) # maximum number of lines to check; includes comment lines if self.displayable( dataset ): try: - seqid = '' - start = 2147483647 # Maximum value of a signed 32 bit integer ( 2**31 - 1 ) + seqid = None + start = sys.maxint stop = 0 - for i, line in enumerate( file( dataset.file_name ) ): - line = line.rstrip( '\r\n' ) - if not line: - continue - if line.startswith( '##sequence-region' ): # ##sequence-region IV 6000000 6030000 - elems = line.split() - if len( elems ) > 3: - # line looks like: - # ##sequence-region ctg123 1 1497228 - seqid = elems[1] # IV - start = elems[2] # 6000000 - stop = elems[3] # 6030000 - break - elif len( elems ) == 2 and elems[1].find( '..' ) > 0: - # line looks like this: - # ##sequence-region X:120000..140000 - elems = elems[1].split( ':' ) - seqid = elems[0] - start = elems[1].split( '..' )[0] - stop = elems[1].split( '..' )[1] - break - else: - log.exception( "line (%s) uses an unsupported ##sequence-region definition." % str( line ) ) - break - # Allow UCSC style browser and track info in the GFF file - if line.startswith("browser position"): - pos_info = line.split()[-1] - seqid, startend = pos_info.split(":") - start, end = startend.split("-") + fh = open( dataset.file_name ) + while True: + line = fh.readline( VIEWPORT_READLINE_BUFFER_SIZE ) + if not line: break #EOF + try: + if line.startswith( '##sequence-region' ): # ##sequence-region IV 6000000 6030000 + elems = line.rstrip( '\n\r' ).split() + if len( elems ) > 3: + # line looks like: + # ##sequence-region ctg123 1 1497228 + seqid = elems[1] # IV + start = int( elems[2] )# 6000000 + stop = int( elems[3] ) # 6030000 + break #use location declared in file + elif len( elems ) == 2 and elems[1].find( '..' ) > 0: + # line looks like this: + # ##sequence-region X:120000..140000 + elems = elems[1].split( ':' ) + seqid = elems[0] + start = int( elems[1].split( '..' )[0] ) + stop = int( elems[1].split( '..' )[1] ) + break #use location declared in file + else: + log.exception( "line (%s) uses an unsupported ##sequence-region definition." % str( line ) ) + #break #no break, if bad definition, we try another method + elif line.startswith("browser position"): + # Allow UCSC style browser and track info in the GFF file + pos_info = line.split()[-1] + seqid, startend = pos_info.split(":") + start, stop = map( int, startend.split("-") ) + break #use location declared in file + elif True not in map( line.startswith, ( '#', 'track', 'browser' ) ):# line.startswith() does not accept iterator in python2.4 + viewport_feature_count -= 1 + elems = line.rstrip( '\n\r' ).split( '\t' ) + if len( elems ) > 3: + 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[3] ) ) + stop = max( stop, int( elems[4] ) ) + except: + #most likely start/stop is not an int or not enough fields + pass + #make sure we are at the next new line + readline_count = VIEWPORT_MAX_READS_PER_LINE + while line.rstrip( '\n\r' ) == line: + assert readline_count > 0, Exception( 'Viewport readline count exceeded for dataset %s.' % dataset.id ) + line = fh.readline( VIEWPORT_READLINE_BUFFER_SIZE ) + if not line: break #EOF + readline_count -= 1 + max_line_count -= 1 + if not viewport_feature_count or not max_line_count: + #exceeded viewport or total line count to check break - if not line.startswith(('#', 'track', 'browser')) : - elems = line.split( '\t' ) - 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[3] ) ) - stop = max( stop, int( elems[4] ) ) - else: - # We've spanned a chromosome - break - if i > 10: - break + if seqid is not None: + return ( seqid, str( start ), str( stop ) ) #Necessary to return strings? except Exception, e: + #unexpected error log.exception( str( e ) ) - return ( None, None, None ) - return ( seqid, str( start ), str( stop ) ) - else: - return ( None, None, None ) + return ( None, None, None ) #could not determine viewport def ucsc_links( self, dataset, type, app, base_url ): ret_val = [] seqid, start, stop = self.get_estimated_display_viewport( dataset ) @@ -963,44 +965,67 @@ class Wiggle( Tabular, _RemoteCallMixin Tabular.__init__( self, **kwd ) self.add_display_app( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' ) self.add_display_app( 'gbrowse', 'display in Gbrowse', 'as_gbrowse_display_file', 'gbrowse_links' ) - def get_estimated_display_viewport( self, dataset ): + """Return a chrom, start, stop tuple for viewing a file.""" + viewport_feature_count = 100 # viewport should check at least 100 features; excludes comment lines + max_line_count = max( viewport_feature_count, 500 ) # maximum number of lines to check; includes comment lines if self.displayable( dataset ): - num_check_lines = 100 # only check up to this many non empty lines - vstart = None - vend = 0 - vwig_chr = '?' - value = None - for i, line in enumerate( file( dataset.file_name ) ): - line = line.rstrip( '\r\n' ) - if line: - if line.startswith( "browser" ): - chr_info = line.split()[-1] - wig_chr, coords = chr_info.split( ":" ) - start, end = coords.split( "-" ) - value = ( wig_chr, start, end ) + try: + chrom = None + start = sys.maxint + end = 0 + span = 1 + step = None + fh = open( dataset.file_name ) + while True: + line = fh.readline( VIEWPORT_READLINE_BUFFER_SIZE ) + if not line: break #EOF + try: + if line.startswith( "browser" ): + chr_info = line.rstrip( '\n\r' ).split()[-1] + chrom, coords = chr_info.split( ":" ) + start, end = map( int, coords.split( "-" ) ) + break # use the browser line + # variableStep chrom=chr20 + if line and ( line.lower().startswith( "variablestep" ) or line.lower().startswith( "fixedstep" ) ): + if chrom is not None: break #different chrom or different section of the chrom + chrom = line.rstrip( '\n\r' ).split("chrom=")[1].split()[0] + if 'span=' in line: + span = int( line.rstrip( '\n\r' ).split("span=")[1].split()[0] ) + if 'step=' in line: + step = int( line.rstrip( '\n\r' ).split("step=")[1].split()[0] ) + start = int( line.rstrip( '\n\r' ).split("start=")[1].split()[0] ) + else: + fields = line.rstrip( '\n\r' ).split() + if fields: + if step is not None: + if not end: + end = start + span + else: + end += step + else: + start = min( int( fields[0] ), start ) + end = max( end, int( fields[0] ) + span ) + viewport_feature_count -= 1 + except: + pass + #make sure we are at the next new line + readline_count = VIEWPORT_MAX_READS_PER_LINE + while line.rstrip( '\n\r' ) == line: + assert readline_count > 0, Exception( 'Viewport readline count exceeded for dataset %s.' % dataset.id ) + line = fh.readline( VIEWPORT_READLINE_BUFFER_SIZE ) + if not line: break #EOF + readline_count -= 1 + max_line_count -= 1 + if not viewport_feature_count or not max_line_count: + #exceeded viewport or total line count to check break - # variableStep chrom=chr20 - if line and (line.lower().startswith( "variablestep" ) or line.lower().startswith( "fixedstep" )): - c = line.split("chr")[-1] - c = c.split()[0] - vwig_chr = 'chr%s' % c - else: - try: - offset = line.split()[0] - offset = int(offset) - vend = max(vend,offset) - if not vstart: - vstart = offset # first - except: - pass - if i > num_check_lines: - break - if value == None: - value = (vwig_chr, vstart, vend) - return value - else: - return ( None, None, None ) + if chrom is not None: + return ( chrom, str( start ), str( end ) ) #Necessary to return strings? + except Exception, e: + #unexpected error + log.exception( str( e ) ) + return ( None, None, None ) #could not determine viewport def gbrowse_links( self, dataset, type, app, base_url ): ret_val = [] chrom, start, stop = self.get_estimated_display_viewport( dataset ) @@ -1119,44 +1144,61 @@ class CustomTrack ( Tabular ): def display_peek( self, dataset ): """Returns formated html of peek""" return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] ) - def get_estimated_display_viewport( self, dataset ): + def get_estimated_display_viewport( self, dataset, chrom_col = None, start_col = None, end_col = None ): + """Return a chrom, start, stop tuple for viewing a file.""" + #FIXME: only BED and WIG custom tracks are currently supported + #As per previously existing behavior, viewport will only be over the first intervals + max_line_count = 100 # maximum number of lines to check; includes comment lines + variable_step_wig = False + chrom = None + span = 1 if self.displayable( dataset ): try: - wiggle_format = False - for line in open(dataset.file_name): - if (line.startswith("chr") or line.startswith("scaffold")): - line = line.rstrip( '\n\r' ) - start = line.split("\t")[1].replace(",","") - end = line.split("\t")[2].replace(",","") - - if int(start) < int(end): - value = ( line.split("\t")[0], start, end ) - else: - value = ( line.split("\t")[0], end, start ) - + fh = open( dataset.file_name ) + while True: + line = fh.readline( VIEWPORT_READLINE_BUFFER_SIZE ) + if not line: break #EOF + if not line.startswith( '#' ): + try: + if variable_step_wig: + fields = line.rstrip().split() + if len( fields ) == 2: + start = int( fields[ 0 ] ) + return ( chrom, str( start ), str( start + span ) ) + elif line and ( line.lower().startswith( "variablestep" ) or line.lower().startswith( "fixedstep" ) ): + chrom = line.rstrip( '\n\r' ).split("chrom=")[1].split()[0] + if 'span=' in line: + span = int( line.rstrip( '\n\r' ).split("span=")[1].split()[0] ) + if 'start=' in line: + start = int( line.rstrip( '\n\r' ).split("start=")[1].split()[0] ) + return ( chrom, str( start ), str( start + span ) ) + else: + variable_step_wig = True + else: + fields = line.rstrip().split( '\t' ) + if len( fields ) >= 3: + chrom = fields[ 0 ] + start = int( fields[ 1 ] ) + end = int( fields[ 2 ] ) + return ( chrom, str( start ), str( end ) ) + except Exception: + #most likely a non-integer field has been encountered for start / stop + continue + #make sure we are at the next new line + readline_count = VIEWPORT_MAX_READS_PER_LINE + while line.rstrip( '\n\r' ) == line: + assert readline_count > 0, Exception( 'Viewport readline count exceeded for dataset %s.' % dataset.id ) + line = fh.readline( VIEWPORT_READLINE_BUFFER_SIZE ) + if not line: break #EOF + readline_count -= 1 + max_line_count -= 1 + if not max_line_count: + #exceeded viewport or total line count to check break - - elif (line.startswith('variableStep')): - # wiggle format - wiggle_format = True - wig_chr = line.split()[1].split('=')[1] - if not wig_chr.startswith("chr"): - value = ('', '', '') - break - elif wiggle_format: - # wiggle format - if line.split("\t")[0].isdigit(): - start = line.split("\t")[0] - end = str(int(start) + 1) - value = (wig_chr, start, end) - else: - value = (wig_chr, '', '') - break - return value #returns the co-ordinates of the 1st track/dataset - except: - return ( None, None, None ) - else: - return ( None, None, None ) + except Exception, e: + #unexpected error + log.exception( str( e ) ) + return ( None, None, None ) #could not determine viewport def ucsc_links( self, dataset, type, app, base_url ): ret_val = [] chrom, start, stop = self.get_estimated_display_viewport(dataset)