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Fix for 1 line interval files that do not include a commented header. Added default values for chrom, start, end for interval format and enhanced set_meta() so that auto-detect button on edit form will work for interval files.
This commit is contained in:
Greg Von Kuster
@@ -41,9 +41,9 @@ class Interval( Tabular ):
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file_ext = "interval"
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"""Add metadata elements"""
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MetadataElement( name="chromCol", desc="Chrom column", param=metadata.ColumnParameter )
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MetadataElement( name="startCol", desc="Start column", param=metadata.ColumnParameter )
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MetadataElement( name="endCol", desc="End column", param=metadata.ColumnParameter )
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MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter )
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MetadataElement( name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter )
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MetadataElement( name="endCol", default=3, desc="End column", param=metadata.ColumnParameter )
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MetadataElement( name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0 )
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MetadataElement( name="nameCol", desc="Name/Identifier column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0 )
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MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False )
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@@ -59,33 +59,62 @@ class Interval( Tabular ):
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def set_peek( self, dataset ):
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"""Set the peek and blurb text"""
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dataset.peek = data.get_file_peek( dataset.file_name )
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## dataset.peek = self.make_html_table( dataset.peek )
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dataset.blurb = util.commaify( str( data.get_line_count( dataset.file_name ) ) ) + " regions"
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#i don't think set_meta should not be called here, it should be called separately
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#self.set_meta( dataset )
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def set_meta( self, dataset, first_line_is_header=False ):
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Tabular.set_meta( self, dataset, 1 )
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Tabular.set_meta( self, dataset, skip=0 )
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"""Tries to guess from the line the location number of the column for the chromosome, region start-end and strand"""
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if dataset.has_data():
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for i, line in enumerate( file(dataset.file_name) ):
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line = line.rstrip('\r\n')
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if len(line)>0:
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if (first_line_is_header or line[0] == '#'):
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self.init_meta(dataset)
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line = line.strip("#")
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elems = line.split("\t")
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valid = dict(alias_helper) # shrinks
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for index, col_name in enumerate(elems):
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for i, line in enumerate( file( dataset.file_name ) ):
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line = line.rstrip( '\r\n' )
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if line:
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if ( first_line_is_header or line[0] == '#' ):
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self.init_meta( dataset )
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line = line.strip( '#' )
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elems = line.split( '\t' )
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valid = dict( alias_helper ) # shrinks
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for index, col_name in enumerate( elems ):
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if col_name in valid:
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meta_name = valid[col_name]
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setattr(dataset.metadata, meta_name, index+1)
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values = alias_spec[meta_name]
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start = values.index(col_name)
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for lower in values[start:]:
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del valid[lower] # removes lower priority keys
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setattr( dataset.metadata, meta_name, index+1 )
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values = alias_spec[ meta_name ]
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start = values.index( col_name )
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for lower in values[ start: ]:
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del valid[ lower ] # removes lower priority keys
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break # Our metadata is set, so break out of the outer loop
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else:
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# Header lines in Interval files are optional. For example, BED is Interval but has no header.
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# We'll make a best guess at the location of the metadata columns.
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metadata_is_set = False
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elems = line.split( '\t' )
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if len( elems ) > 2:
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for str in data.col1_startswith:
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if line.lower().startswith( str ):
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dataset.metadata.chromCol = 1
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try:
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int( elems[1] )
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dataset.metadata.startCol = 2
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except:
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pass # Metadata default will be used
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try:
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int( elems[2] )
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dataset.metadata.endCol = 3
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except:
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pass # Metadata default will be used
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if len( elems ) > 3:
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try:
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int( elems[3] )
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except:
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dataset.metadata.nameCol = 4
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if len( elems ) < 6:
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dataset.metadata.strandCol = 0
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else:
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dataset.metadata.strandCol = 6
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metadata_is_set = True
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break
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if metadata_is_set:
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break # Our metadata is set, so break out of the outer loop
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def get_estimated_display_viewport( self, dataset ):
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"""Return a chrom, start, stop tuple for viewing a file."""
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@@ -202,7 +231,7 @@ class Interval( Tabular ):
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so we'll just look for some valid data.
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"""
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for hdr in headers:
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if not (hdr[0] == '' or hdr[0].startswith( '#' )):
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if hdr and not hdr[0].startswith( '#' ):
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if len(hdr) < 3:
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return False
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try:
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@@ -2,9 +2,11 @@
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Classes related to parameter validation.
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"""
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import re
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import re, logging
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from elementtree.ElementTree import XML
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log = logging.getLogger( __name__ )
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class Validator( object ):
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"""
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A validator checks that a value meets some conditions OR raises ValueError
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@@ -146,7 +148,7 @@ class MetadataValidator( Validator ):
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"""
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def validate( self, value, history=None ):
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if value.missing_meta():
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raise ValueError( "you are missing required metadata" )
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raise ValueError( "Metadata missing, click the pencil icon in the history item to edit / save the metadata attributes" )
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validator_types = dict( expression=ExpressionValidator,
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regex=RegexValidator,
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