def __init__(self, options, log_info=None): #{
BasePredictorCls.__init__(self, 'fusion', 'fus', 'fusion',
options, log_info=log_info)
#dup_gene_path = GetFilePath(options.output_dir, options.lib,
# "%s.dup_genes" % self.ext)
#self.dup_gene_file = FileBoxCls(dup_gene_path, "w",
# "cannot create duplicated gene %s output file" % self.description)
#mix_dir_path = GetFilePath(options.output_dir, options.lib,
# "%s.mix_dirs" % self.ext)
#self.mix_dir_file = FileBoxCls(mix_dir_path, "w",
# "cannot create mixed gene directions %s output file" % self.description)
self.AddOutFile("dup_gene", "%s.dup_genes" % self.ext,
"duplicated gene %s" % self.description)
self.AddOutFile("mix_dirs", "%s.mix_dirs" % self.ext,
"mixed sense %s" % self.description)
# TEMPORARY file to keep track of contigs for which one side is missing
# from the realignment results
self.AddOutFile("align_miss", "%s.align_miss.tmp" % self.ext,
"missing realignment %s" % self.description)
# file for potential "read-through" type events
self.AddOutFile("readthru", "%s.rth" % self.ext,
"read-through %s" % self.description)
# gene_directions[id_type][id] = {+,-,*} where "*" = both directions
self.gene_directions = {'gene_name':dict(), 'transcript_id':dict()}
# get gene directions from annotation file
if (self.options.use_gene_directions): #{
self.GetGeneDirections()
#} end if
self.bad_topologies = set([
'end-duplication',
'junction-duplication',
])
def __init__(self, options, log_info=None): #{
BasePredictorCls.__init__(self, 'ptd', 'ptd', 'partial tandem duplication',
options, log_info=log_info)
self.good_topologies = set([
'end-duplication',
'intrachr-non-colinear',
'junction-duplication',
])
def __init__(self, options, log_info=None): #{
BasePredictorCls.__init__(self, 'itd', 'itd',
'internal tandem duplication', options, log_info=log_info)
self.good_topologies = set([
'gap-tandem-duplication',
'gap-nontandem-duplication',
])
if (options.allow_non_gap_itds): #{
self.good_topologies.update([
'end-duplication',
'intrachr-non-colinear',
'junction-duplication',
])
#} end if
#self.store_seq = True
#multi_exon_path = GetFilePath(options.output_dir, options.lib,
# "%s.multi_exon" % self.ext)
#self.multi_exon_file = FileBoxCls(multi_exon_path, "w", "cannot "
# "create multiple exon duplication %s output file" % self.description)
#full_ctg_dup_path = GetFilePath(options.output_dir, options.lib,
# "%s.full_ctg_dup" % self.ext)
#self.full_ctg_dup_file = FileBoxCls(full_ctg_dup_path, "w", "cannot "
# "create full contig duplication %s output file" % self.description)
#edge_gap_path = GetFilePath(options.output_dir, options.lib,
# "%s.edge_gap" % self.ext)
#self.edge_gap_file = FileBoxCls(edge_gap_path, "w", "cannot create "
# "edge-gap duplication %s output file" % self.description)
self.AddOutFile("internal_me", "%s.multi_exon" % self.ext,
"multiple exon duplication %s" % self.description)
self.AddOutFile("edge", "%s.edge_gap" % self.ext,
"edge-gap duplication %s" % self.description)
self.AddOutFile("edge_me", "%s.edge_gap.multi_exon" % self.ext,
"edge-gap multiple exon duplication %s" % self.description)
self.AddOutFile("full", "%s.full_ctg_dup" % self.ext,
"full contig duplication %s" % self.description)
self.AddOutFile("full_me", "%s.full_ctg_dup.multi_exon" % self.ext,
"multiple exon full contig duplication %s" % self.description)
self.num_over_aligned = 0