def LoadExonBoundaryCoordinatesFromFile(self, path): #{
DebugMsg(self, "Gene annotation file: %s" % path)
# open the annotations file
annotations_file = GeneAnnotationParserCls(path, log_info=self.log_info)
skipped_chroms = set()
# get the coordinates from the file
for transcript in annotations_file: #{
# fix chromosome names, if needed
chrom = NormalizeChrID(transcript.chrom)
if (NonStandardChr(chrom)): #{
ExtremeDebugMsg(self, "Skipping transcript in strange chromosome: "
"%s (%s)" % (chrom, transcript.chrom))
skipped_chroms.add(chrom)
continue
#} end if
prev_exon = None
for (index, exon) in enumerate(transcript.SortedExons()): #{
(exon.left, exon.right) = (exon.min, exon.max)
# assume that exon list is sorted by left coordinate
if (None != prev_exon and prev_exon.min > exon.min): #{
raise ExonBoundCounterError("Transcript %s exons are not in "
"order: %s, %s" % (transcript.transcript_id,
prev_exon.ToString(), exon.ToString()))
#} end if
prev_exon = exon
# do not include the left side of the first exon
if (0 == index): #{
exon.left = None
#} end if
# do not include the right side of the last exon
if (len(transcript.exons) == (index+1)): #{
exon.right = None
#} end if
# exon_bound_coords[chrom][prime_side][coord1][coord2] = gene_list
for side in SIDES: #{
if (None != getattr(exon, side)): #{
keys = [chrom, side, getattr(exon, side),
getattr(exon, OtherSide(side))]
AddToMultiDict(self.exon_bound_coords, keys,
transcript.transcript_id)
#} end if
#} end for
#} end for
#} end for
if (0 < len(skipped_chroms)): #{
DebugMsg(self, "Skipped transcripts in chromosomes: %s" %
", ".join(sorted(skipped_chroms)))
#} end if
# close the file
annotations_file.close()
def __init__(self, path, log_info=None): #{
self.log_info = log_info
# open the annotations file
self.parser = GeneAnnotationParserCls(path, log_info=log_info)
class AnnotationsFileCls: #{
def __init__(self, path, log_info=None): #{
self.log_info = log_info
# open the annotations file
self.parser = GeneAnnotationParserCls(path, log_info=log_info)
#} end def
def __iter__(self): #{
return self
#} end def
def next(self): #{
# replace spaces in the alias and
# get rid of any "chr" in the chromosome name
transcript = FixAnnotation(self.parser.next(), use_chr=False)
ExtremeDebugMsg(self, "T: %s" % transcript)
# ensure that the transcript is from a "normal" chromosome,
# not including mitochondrial DNA, and is not a tRNA or rRNA
while (NonStandardChr(transcript.chrom) or
"M" == transcript.chrom or
transcript.gene_name.lower().startswith("trna_") or
transcript.gene_name.lower().endswith("_rrna")): #{
ExtremeDebugMsg(self, " Skipping...")
transcript = FixAnnotation(self.parser.next(), use_chr=False)
ExtremeDebugMsg(self, "T: %s" % transcript)
#} end while
transcript.isoform = 1
# check whether the transcript is coding or non-coding
if (transcript.cdsStart >= transcript.cdsEnd): #{
transcript.non_coding = True
#} end if
# separate the exons into UTRs and coding exons
self.SeparateUTRs(transcript)
# reverse the order of the exons if
# the transcript is on the negative strand
if ("-" == transcript.strand): #{
transcript.exons.reverse()
transcript.split_exons.reverse()
transcript.utr_flags.reverse()
#} end if
return transcript
#} end def
def SeparateUTRs(self, transcript): #{
# ensure that exons are ordered by start coordinate
if (transcript.exons[0][0] > transcript.exons[-1][0]): #{
transcript.exons.reverse()
#} end if
transcript.num_coding_exons = 0
transcript.utr_flags = list()
transcript.split_exons = list()
if (transcript.non_coding): #{
ExtremeDebugMsg(self, "Not separating UTRs for non-coding gene")
return
#} end if
ExtremeDebugMsg(self, "Separating UTRs from coding exons...\n"
"cdsStart: %i, cdsEnd: %i" % (transcript.cdsStart, transcript.cdsEnd))
for (e_start, e_end) in transcript.exons: #{
ExtremeDebugMsg(self, "Exon start: %i, end: %i" % (e_start, e_end))
# if the exon ends before the CDS start or
# the exon starts after the CDS end,
# the full exon is a UTR
if (e_end < transcript.cdsStart or transcript.cdsEnd < e_start): #{
transcript.utr_flags.append(True)
transcript.split_exons.append([e_start, e_end])
ExtremeDebugMsg(self, " full UTR")
else:
# if the exon starts before the CDS start and
# ends after the CDS start,
# the first part of the exon is a UTR
if (e_start < transcript.cdsStart): #{
transcript.utr_flags.append(True)
transcript.split_exons.append([e_start, transcript.cdsStart-1])
e_start = transcript.cdsStart
ExtremeDebugMsg(self, " UTR start: %i-%i\n New start: %i" %
(transcript.split_exons[-1][0],
transcript.split_exons[-1][1], e_start))
#} end if
# if the exon starts before the CDS end and
# ends after the CDS end,
# the second part of the exon is a UTR
if (transcript.cdsEnd < e_end): #{
transcript.num_coding_exons += 1
transcript.utr_flags.append(False)
transcript.split_exons.append([e_start, transcript.cdsEnd])
transcript.utr_flags.append(True)
transcript.split_exons.append([transcript.cdsEnd+1, e_end])
ExtremeDebugMsg(self, " exon start: %i-%i\n UTR end: %i-%i" %
(transcript.split_exons[-2][0], transcript.split_exons[-2][1],
transcript.split_exons[-1][0], transcript.split_exons[-1][1]))
# if the exon starts after the CDS start and
# ends before the CDS end,
# the full exon is really an exon
elif (e_start <= e_end):
transcript.num_coding_exons += 1
transcript.utr_flags.append(False)
transcript.split_exons.append([e_start, e_end])
ExtremeDebugMsg(self, " full exon: %i-%i" % (e_start, e_end))
else:
raise ExonCoordsError("cannot determine exon type: "
"%s: CDS:%i-%i, Exon:%i-%i" % (transcript.alias,
transcript.cdsStart, transcript.cdsEnd, e_start, e_end))
#} end if
#} end if
#} end for
if (len(transcript.split_exons) != len(transcript.utr_flags)): #{
raise ChimeraSimulatorError("error loading transcript: # exons (%i)" %
len(transcript.exons) + " not equal to # UTR flags (%i)" %
len(transcript.utr_flags))
