intersect: utils/gff_util.py annotate

annotate utils/gff_util.py @ 4:8ddabc73af92 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62

author	devteam
date	Thu, 11 Feb 2016 12:11:25 -0500
parents
children	33b3f3688db4

rev	line source
4 8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	1 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	2 Provides utilities for working with GFF files.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	3 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	4
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	5 import copy
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	6 from bx.intervals.io import GenomicInterval, GenomicIntervalReader, MissingFieldError, NiceReaderWrapper
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	7 from bx.tabular.io import Header, Comment, ParseError
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	8 from utils.odict import odict
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	9
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	10
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	11 class GFFInterval( GenomicInterval ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	12 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	13 A GFF interval, including attributes. If file is strictly a GFF file,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	14 only attribute is 'group.'
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	15 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	16 def __init__( self, reader, fields, chrom_col=0, feature_col=2, start_col=3, end_col=4,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	17 strand_col=6, score_col=5, default_strand='.', fix_strand=False ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	18 # HACK: GFF format allows '.' for strand but GenomicInterval does not. To get around this,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	19 # temporarily set strand and then unset after initing GenomicInterval.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	20 unknown_strand = False
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	21 if not fix_strand and fields[ strand_col ] == '.':
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	22 unknown_strand = True
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	23 fields[ strand_col ] = '+'
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	24 GenomicInterval.__init__( self, reader, fields, chrom_col, start_col, end_col, strand_col,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	25 default_strand, fix_strand=fix_strand )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	26 if unknown_strand:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	27 self.strand = '.'
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	28 self.fields[ strand_col ] = '.'
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	29
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	30 # Handle feature, score column.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	31 self.feature_col = feature_col
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	32 if self.feature_col >= self.nfields:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	33 raise MissingFieldError( "No field for feature_col (%d)" % feature_col )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	34 self.feature = self.fields[ self.feature_col ]
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	35 self.score_col = score_col
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	36 if self.score_col >= self.nfields:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	37 raise MissingFieldError( "No field for score_col (%d)" % score_col )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	38 self.score = self.fields[ self.score_col ]
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	39
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	40 # GFF attributes.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	41 self.attributes = parse_gff_attributes( fields[8] )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	42
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	43 def copy( self ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	44 return GFFInterval(self.reader, list( self.fields ), self.chrom_col, self.feature_col, self.start_col,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	45 self.end_col, self.strand_col, self.score_col, self.strand)
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	46
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	47
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	48 class GFFFeature( GFFInterval ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	49 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	50 A GFF feature, which can include multiple intervals.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	51 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	52 def __init__( self, reader, chrom_col=0, feature_col=2, start_col=3, end_col=4,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	53 strand_col=6, score_col=5, default_strand='.', fix_strand=False, intervals=[],
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	54 raw_size=0 ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	55 # Use copy so that first interval and feature do not share fields.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	56 GFFInterval.__init__( self, reader, copy.deepcopy( intervals[0].fields ), chrom_col, feature_col,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	57 start_col, end_col, strand_col, score_col, default_strand,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	58 fix_strand=fix_strand )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	59 self.intervals = intervals
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	60 self.raw_size = raw_size
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	61 # Use intervals to set feature attributes.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	62 for interval in self.intervals:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	63 # Error checking. NOTE: intervals need not share the same strand.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	64 if interval.chrom != self.chrom:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	65 raise ValueError( "interval chrom does not match self chrom: %s != %s" %
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	66 ( interval.chrom, self.chrom ) )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	67 # Set start, end of interval.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	68 if interval.start < self.start:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	69 self.start = interval.start
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	70 if interval.end > self.end:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	71 self.end = interval.end
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	72
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	73 def name( self ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	74 """ Returns feature's name. """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	75 name = None
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	76 # Preference for name: GTF, GFF3, GFF.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	77 for attr_name in ['gene_id', 'transcript_id', # GTF
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	78 'ID', 'id', # GFF3
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	79 'group' ]: # GFF (TODO)
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	80 name = self.attributes.get( attr_name, None )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	81 if name is not None:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	82 break
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	83 return name
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	84
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	85 def copy( self ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	86 intervals_copy = []
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	87 for interval in self.intervals:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	88 intervals_copy.append( interval.copy() )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	89 return GFFFeature(self.reader, self.chrom_col, self.feature_col, self.start_col, self.end_col, self.strand_col,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	90 self.score_col, self.strand, intervals=intervals_copy )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	91
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	92 def lines( self ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	93 lines = []
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	94 for interval in self.intervals:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	95 lines.append( '\t'.join( interval.fields ) )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	96 return lines
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	97
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	98
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	99 class GFFIntervalToBEDReaderWrapper( NiceReaderWrapper ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	100 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	101 Reader wrapper that reads GFF intervals/lines and automatically converts
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	102 them to BED format.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	103 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	104
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	105 def parse_row( self, line ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	106 # HACK: this should return a GFF interval, but bx-python operations
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	107 # require GenomicInterval objects and subclasses will not work.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	108 interval = GenomicInterval( self, line.split( "\t" ), self.chrom_col, self.start_col,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	109 self.end_col, self.strand_col, self.default_strand,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	110 fix_strand=self.fix_strand )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	111 interval = convert_gff_coords_to_bed( interval )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	112 return interval
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	113
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	114
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	115 class GFFReaderWrapper( NiceReaderWrapper ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	116 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	117 Reader wrapper for GFF files.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	118
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	119 Wrapper has two major functions:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	120
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	121 1. group entries for GFF file (via group column), GFF3 (via id attribute),
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	122 or GTF (via gene_id/transcript id);
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	123 2. convert coordinates from GFF format--starting and ending coordinates
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	124 are 1-based, closed--to the 'traditional'/BED interval format--0 based,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	125 half-open. This is useful when using GFF files as inputs to tools that
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	126 expect traditional interval format.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	127 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	128
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	129 def __init__( self, reader, chrom_col=0, feature_col=2, start_col=3,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	130 end_col=4, strand_col=6, score_col=5, fix_strand=False, convert_to_bed_coord=False, **kwargs ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	131 NiceReaderWrapper.__init__( self, reader, chrom_col=chrom_col, start_col=start_col, end_col=end_col,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	132 strand_col=strand_col, fix_strand=fix_strand, **kwargs )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	133 self.feature_col = feature_col
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	134 self.score_col = score_col
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	135 self.convert_to_bed_coord = convert_to_bed_coord
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	136 self.last_line = None
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	137 self.cur_offset = 0
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	138 self.seed_interval = None
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	139 self.seed_interval_line_len = 0
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	140
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	141 def parse_row( self, line ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	142 interval = GFFInterval( self, line.split( "\t" ), self.chrom_col, self.feature_col,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	143 self.start_col, self.end_col, self.strand_col, self.score_col,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	144 self.default_strand, fix_strand=self.fix_strand )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	145 return interval
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	146
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	147 def next( self ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	148 """ Returns next GFFFeature. """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	149
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	150 #
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	151 # Helper function.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	152 #
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	153
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	154 def handle_parse_error( parse_error ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	155 """ Actions to take when ParseError found. """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	156 if self.outstream:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	157 if self.print_delegate and hasattr(self.print_delegate, "__call__"):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	158 self.print_delegate( self.outstream, e, self )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	159 self.skipped += 1
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	160 # no reason to stuff an entire bad file into memmory
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	161 if self.skipped < 10:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	162 self.skipped_lines.append( ( self.linenum, self.current_line, str( e ) ) )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	163
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	164 # For debugging, uncomment this to propogate parsing exceptions up.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	165 # I.e. the underlying reason for an unexpected StopIteration exception
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	166 # can be found by uncommenting this.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	167 # raise e
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	168
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	169 #
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	170 # Get next GFFFeature
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	171 #
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	172 raw_size = self.seed_interval_line_len
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	173
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	174 # If there is no seed interval, set one. Also, if there are no more
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	175 # intervals to read, this is where iterator dies.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	176 if not self.seed_interval:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	177 while not self.seed_interval:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	178 try:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	179 self.seed_interval = GenomicIntervalReader.next( self )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	180 except ParseError, e:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	181 handle_parse_error( e )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	182 # TODO: When no longer supporting python 2.4 use finally:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	183 #finally:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	184 raw_size += len( self.current_line )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	185
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	186 # If header or comment, clear seed interval and return it with its size.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	187 if isinstance( self.seed_interval, ( Header, Comment ) ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	188 return_val = self.seed_interval
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	189 return_val.raw_size = len( self.current_line )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	190 self.seed_interval = None
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	191 self.seed_interval_line_len = 0
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	192 return return_val
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	193
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	194 # Initialize feature identifier from seed.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	195 feature_group = self.seed_interval.attributes.get( 'group', None ) # For GFF
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	196 # For GFF3
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	197 feature_id = self.seed_interval.attributes.get( 'ID', None )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	198 # For GTF.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	199 feature_transcript_id = self.seed_interval.attributes.get( 'transcript_id', None )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	200
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	201 # Read all intervals associated with seed.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	202 feature_intervals = []
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	203 feature_intervals.append( self.seed_interval )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	204 while True:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	205 try:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	206 interval = GenomicIntervalReader.next( self )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	207 raw_size += len( self.current_line )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	208 except StopIteration, e:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	209 # No more intervals to read, but last feature needs to be
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	210 # returned.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	211 interval = None
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	212 raw_size += len( self.current_line )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	213 break
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	214 except ParseError, e:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	215 handle_parse_error( e )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	216 raw_size += len( self.current_line )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	217 continue
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	218 # TODO: When no longer supporting python 2.4 use finally:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	219 #finally:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	220 #raw_size += len( self.current_line )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	221
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	222 # Ignore comments.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	223 if isinstance( interval, Comment ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	224 continue
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	225
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	226 # Determine if interval is part of feature.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	227 part_of = False
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	228 group = interval.attributes.get( 'group', None )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	229 # GFF test:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	230 if group and feature_group == group:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	231 part_of = True
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	232 # GFF3 test:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	233 parent_id = interval.attributes.get( 'Parent', None )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	234 cur_id = interval.attributes.get( 'ID', None )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	235 if ( cur_id and cur_id == feature_id ) or ( parent_id and parent_id == feature_id ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	236 part_of = True
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	237 # GTF test:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	238 transcript_id = interval.attributes.get( 'transcript_id', None )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	239 if transcript_id and transcript_id == feature_transcript_id:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	240 part_of = True
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	241
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	242 # If interval is not part of feature, clean up and break.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	243 if not part_of:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	244 # Adjust raw size because current line is not part of feature.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	245 raw_size -= len( self.current_line )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	246 break
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	247
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	248 # Interval associated with feature.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	249 feature_intervals.append( interval )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	250
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	251 # Last interval read is the seed for the next interval.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	252 self.seed_interval = interval
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	253 self.seed_interval_line_len = len( self.current_line )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	254
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	255 # Return feature.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	256 feature = GFFFeature( self, self.chrom_col, self.feature_col, self.start_col,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	257 self.end_col, self.strand_col, self.score_col,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	258 self.default_strand, fix_strand=self.fix_strand,
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	259 intervals=feature_intervals, raw_size=raw_size )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	260
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	261 # Convert to BED coords?
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	262 if self.convert_to_bed_coord:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	263 convert_gff_coords_to_bed( feature )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	264
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	265 return feature
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	266
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	267
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	268 def convert_bed_coords_to_gff( interval ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	269 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	270 Converts an interval object's coordinates from BED format to GFF format.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	271 Accepted object types include GenomicInterval and list (where the first
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	272 element in the list is the interval's start, and the second element is
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	273 the interval's end).
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	274 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	275 if isinstance( interval, GenomicInterval ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	276 interval.start += 1
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	277 if isinstance( interval, GFFFeature ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	278 for subinterval in interval.intervals:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	279 convert_bed_coords_to_gff( subinterval )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	280 elif type( interval ) is list:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	281 interval[ 0 ] += 1
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	282 return interval
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	283
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	284
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	285 def convert_gff_coords_to_bed( interval ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	286 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	287 Converts an interval object's coordinates from GFF format to BED format.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	288 Accepted object types include GFFFeature, GenomicInterval, and list (where
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	289 the first element in the list is the interval's start, and the second
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	290 element is the interval's end).
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	291 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	292 if isinstance( interval, GenomicInterval ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	293 interval.start -= 1
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	294 if isinstance( interval, GFFFeature ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	295 for subinterval in interval.intervals:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	296 convert_gff_coords_to_bed( subinterval )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	297 elif type( interval ) is list:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	298 interval[ 0 ] -= 1
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	299 return interval
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	300
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	301
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	302 def parse_gff_attributes( attr_str ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	303 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	304 Parses a GFF/GTF attribute string and returns a dictionary of name-value
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	305 pairs. The general format for a GFF3 attributes string is
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	306
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	307 name1=value1;name2=value2
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	308
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	309 The general format for a GTF attribute string is
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	310
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	311 name1 "value1" ; name2 "value2"
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	312
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	313 The general format for a GFF attribute string is a single string that
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	314 denotes the interval's group; in this case, method returns a dictionary
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	315 with a single key-value pair, and key name is 'group'
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	316 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	317 attributes_list = attr_str.split(";")
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	318 attributes = {}
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	319 for name_value_pair in attributes_list:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	320 # Try splitting by '=' (GFF3) first because spaces are allowed in GFF3
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	321 # attribute; next, try double quotes for GTF.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	322 pair = name_value_pair.strip().split("=")
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	323 if len( pair ) == 1:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	324 pair = name_value_pair.strip().split("\"")
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	325 if len( pair ) == 1:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	326 # Could not split for some reason -- raise exception?
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	327 continue
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	328 if pair == '':
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	329 continue
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	330 name = pair[0].strip()
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	331 if name == '':
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	332 continue
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	333 # Need to strip double quote from values
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	334 value = pair[1].strip(" \"")
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	335 attributes[ name ] = value
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	336
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	337 if len( attributes ) == 0:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	338 # Could not split attributes string, so entire string must be
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	339 # 'group' attribute. This is the case for strictly GFF files.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	340 attributes['group'] = attr_str
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	341 return attributes
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	342
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	343
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	344 def gff_attributes_to_str( attrs, gff_format ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	345 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	346 Convert GFF attributes to string. Supported formats are GFF3, GTF.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	347 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	348 if gff_format == 'GTF':
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	349 format_string = '%s "%s"'
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	350 # Convert group (GFF) and ID, parent (GFF3) attributes to transcript_id, gene_id
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	351 id_attr = None
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	352 if 'group' in attrs:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	353 id_attr = 'group'
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	354 elif 'ID' in attrs:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	355 id_attr = 'ID'
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	356 elif 'Parent' in attrs:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	357 id_attr = 'Parent'
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	358 if id_attr:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	359 attrs['transcript_id'] = attrs['gene_id'] = attrs[id_attr]
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	360 elif gff_format == 'GFF3':
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	361 format_string = '%s=%s'
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	362 attrs_strs = []
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	363 for name, value in attrs.items():
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	364 attrs_strs.append( format_string % ( name, value ) )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	365 return " ; ".join( attrs_strs )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	366
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	367
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	368 def read_unordered_gtf( iterator, strict=False ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	369 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	370 Returns GTF features found in an iterator. GTF lines need not be ordered
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	371 or clustered for reader to work. Reader returns GFFFeature objects sorted
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	372 by transcript_id, chrom, and start position.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	373 """
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	374
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	375 # -- Get function that generates line/feature key. --
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	376
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	377 get_transcript_id = lambda fields: parse_gff_attributes( fields[8] )[ 'transcript_id' ]
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	378 if strict:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	379 # Strict GTF parsing uses transcript_id only to group lines into feature.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	380 key_fn = get_transcript_id
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	381 else:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	382 # Use lenient parsing where chromosome + transcript_id is the key. This allows
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	383 # transcripts with same ID on different chromosomes; this occurs in some popular
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	384 # datasources, such as RefGenes in UCSC.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	385 key_fn = lambda fields: fields[0] + '_' + get_transcript_id( fields )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	386
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	387 # Aggregate intervals by transcript_id and collect comments.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	388 feature_intervals = odict()
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	389 comments = []
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	390 for count, line in enumerate( iterator ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	391 if line.startswith( '#' ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	392 comments.append( Comment( line ) )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	393 continue
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	394
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	395 line_key = key_fn( line.split('\t') )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	396 if line_key in feature_intervals:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	397 feature = feature_intervals[ line_key ]
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	398 else:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	399 feature = []
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	400 feature_intervals[ line_key ] = feature
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	401 feature.append( GFFInterval( None, line.split( '\t' ) ) )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	402
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	403 # Create features.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	404 chroms_features = {}
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	405 for count, intervals in enumerate( feature_intervals.values() ):
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	406 # Sort intervals by start position.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	407 intervals.sort( lambda a, b: cmp( a.start, b.start ) )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	408 feature = GFFFeature( None, intervals=intervals )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	409 if feature.chrom not in chroms_features:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	410 chroms_features[ feature.chrom ] = []
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	411 chroms_features[ feature.chrom ].append( feature )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	412
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	413 # Sort features by chrom, start position.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	414 chroms_features_sorted = []
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	415 for chrom_features in chroms_features.values():
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	416 chroms_features_sorted.append( chrom_features )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	417 chroms_features_sorted.sort( lambda a, b: cmp( a[0].chrom, b[0].chrom ) )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	418 for features in chroms_features_sorted:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	419 features.sort( lambda a, b: cmp( a.start, b.start ) )
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	420
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	421 # Yield comments first, then features.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	422 # FIXME: comments can appear anywhere in file, not just the beginning.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	423 # Ideally, then comments would be associated with features and output
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	424 # just before feature/line.
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	425 for comment in comments:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	426 yield comment
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	427
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	428 for chrom_features in chroms_features_sorted:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	429 for feature in chrom_features:
8ddabc73af92 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit 4e2052686dfe8003f867449e0affff96398b2a62 devteam parents: diff changeset	430 yield feature

Mercurial > repos > devteam > intersect

annotate utils/gff_util.py @ 4:8ddabc73af92 draft