def Run(self): #{
LogMsg(self, "Adding breakpoint gene annotation...")
start = time.time()
group_parser = CandidateGroupParserCls(self.options.barnacle_path)
self.CreateGroupCoordsFile(group_parser)
self.overlaps_stream = RunOverlapCode(self.options.genes_path,
self.options.group_coords_path, STREAM_OUT, dpt=self.options.dpt,
log_info=self.log_info)
self.output_file = FileBoxCls(self.options.out_path, "w",
"cannot create output file")
overlaps_remain = True
for group in group_parser: #{
# get the breakpoint gene annotation for the group
if (overlaps_remain): #{
try: #{
self.GetBreakpointOverlaps(group)
except StopIteration:
DebugMsg(self, "No overlaps remain")
overlaps_remain = False
#} end try
#} end if
# write the group to the output file
self.output_file.Write(group.FullDataString())
#} end for
self.output_file.Close()
if (not self.options.keep_coords_file): #{
os.remove(self.options.group_coords_path)
#} end def
LogMsg(self, "Time spent adding breakpoint gene annotation: %s" %
TimeSpent(start))
class BreakpointGeneAnnotatorCls: #{
def __init__(self, options): #{
SetupMainClass(self, options)
self.overlaps_stream = None
self.curr_overlap = None
self.output_file = None
#} end def
def __del__(self): #{
if (hasattr(self, "output_file") and None != self.output_file): #{
self.output_file.Close()
#} end if
CloseLogFile(self)
#} end def
def Run(self): #{
LogMsg(self, "Adding breakpoint gene annotation...")
start = time.time()
group_parser = CandidateGroupParserCls(self.options.barnacle_path)
self.CreateGroupCoordsFile(group_parser)
self.overlaps_stream = RunOverlapCode(self.options.genes_path,
self.options.group_coords_path, STREAM_OUT, dpt=self.options.dpt,
log_info=self.log_info)
self.output_file = FileBoxCls(self.options.out_path, "w",
"cannot create output file")
overlaps_remain = True
for group in group_parser: #{
# get the breakpoint gene annotation for the group
if (overlaps_remain): #{
try: #{
self.GetBreakpointOverlaps(group)
except StopIteration:
DebugMsg(self, "No overlaps remain")
overlaps_remain = False
#} end try
#} end if
# write the group to the output file
self.output_file.Write(group.FullDataString())
#} end for
self.output_file.Close()
if (not self.options.keep_coords_file): #{
os.remove(self.options.group_coords_path)
#} end def
LogMsg(self, "Time spent adding breakpoint gene annotation: %s" %
TimeSpent(start))
#} end def
def CreateGroupCoordsFile(self, group_parser): #{
if (self.options.use_existing_group_coords): #{
LogMsg(self, "Using existing group coordinates file.")
return
#} end if
# check whether to use "chr" in chromosome names in coordinates file
use_chr = ShouldChromUseChr(1, self.options.genes_path,
"exon coordinates", self.log_info)
# open the group coordinates file
group_coords_file = FileBoxCls(self.options.group_coords_path, "w",
"cannot create event coordinates file")
for group in group_parser: #{
ExtremeDebugMsg(self, "Writing coordinates for group %i" % group.id)
self.WriteGroupCoords(group, group_coords_file, use_chr)
#} end for
group_parser.Close()
group_coords_file.Close()
#} end def
def WriteGroupCoords(self, group, group_coords_file, use_chr): #{
for candidate in group.members: #{
if (candidate.gap): #{
# write gap group coordinates
self.WriteGapGroupCoords(candidate, group_coords_file, use_chr)
else:
# write split group coordinates
self.WriteSplitGroupCoords(candidate, group_coords_file, use_chr)
#} end if
#} end for
#} end def
def WriteGapGroupCoords(self, candidate, group_coords_file, use_chr): #{
gap_coords = ConstructBEDString(candidate.align_info_B.chrom, use_chr,
candidate.align_info_B.genome_start, candidate.align_info_B.genome_end,
"%sA" % candidate.IDString())
group_coords_file.WriteLine(gap_coords)
#} end def
def WriteSplitGroupCoords(self, candidate, group_coords_file, use_chr): #{
#split_coords_A = GroupCoordsCls(candidate.align_info_A.chrom,
# candidate.align_info_A.genome_end - self.options.event_buffer,
# candidate.align_info_A.genome_end + self.options.event_buffer,
# "%sA" % candidate.IDString(), use_chr)
#group_coords_file.WriteLine("%s" % split_coords_A.ToString())
#split_coords_B = GroupCoordsCls(candidate.align_info_B.chrom,
# candidate.align_info_B.genome_start - self.options.event_buffer,
# candidate.align_info_B.genome_start + self.options.event_buffer,
# "%sB" % candidate.IDString(), use_chr)
#group_coords_file.WriteLine("%s" % split_coords_B.ToString())
region_ids = ("A", "B")
for i in [0,1]: #{
genome_coords = (candidate.alignments[i].genome_start,
candidate.alignments[i].genome_end)
split_coords = ConstructBEDString(candidate.alignments[i].chrom, use_chr,
genome_coords[1-i] - self.options.event_buffer,
genome_coords[1-i] + self.options.event_buffer,
"%s%s" % (candidate.IDString(), region_ids[i]))
group_coords_file.WriteLine(split_coords)
#} end for
#} end def
def GetBreakpointOverlaps(self, group): #{
# clear any previous breakpoint genes
group.ClearBPGenes()
# skip overlaps for groups that come before the current group
while (not hasattr(self, "curr_overlap") or None == self.curr_overlap or
self.curr_overlap.group_id < group.id): #{
self.GetNextOverlap()
#} end while
# create a dictionary of the members of the current group
candidates_dict = dict((candidate.candidate_id, candidate) for
candidate in group.members)
# get all overlaps for the current group
while (self.curr_overlap.group_id == group.id): #{
ExtremeDebugMsg(self, "Found overlap for %i%s" %
(self.curr_overlap.group_id, self.curr_overlap.candidate_id))
if (self.curr_overlap.candidate_id in candidates_dict): #{
ExtremeDebugMsg(self, " candidate ID in dictionary!")
self.AddBreakPointGene(candidates_dict[self.curr_overlap.candidate_id])
#} end if
self.GetNextOverlap()
#} end while
#} end def
def GetNextOverlap(self): #{
if (None == self.overlaps_stream): #{
raise BreakpointGeneAnnotatorError("breakpoint gene overlap stream "
"is not open!")
#} end if
overlap_line = CleanLine(self.overlaps_stream.next())
tokenizer = TokenizerCls(overlap_line, delimiter=" ",
log_info=self.log_info)
try:
self.curr_overlap = FeatureOverlapCls(tokenizer, multi_target=True)
except ValueError,e:
raise BreakpointGeneAnnotatorError("error parsing overlap line: "
"%s\n%s" % (overlap_line, e))
# end try
ParseFullEventID(self.curr_overlap, self.curr_overlap.query_id)
