def __init__( self, reader, fields, chrom_col=0, feature_col=2, start_col=3, end_col=4,
strand_col=6, score_col=5, default_strand='.', fix_strand=False ):
# HACK: GFF format allows '.' for strand but GenomicInterval does not. To get around this,
# temporarily set strand and then unset after initing GenomicInterval.
unknown_strand = False
if not fix_strand and fields[ strand_col ] == '.':
unknown_strand = True
fields[ strand_col ] = '+'
GenomicInterval.__init__( self, reader, fields, chrom_col, start_col, end_col, strand_col,
default_strand, fix_strand=fix_strand )
if unknown_strand:
self.strand = '.'
self.fields[ strand_col ] = '.'
# Handle feature, score column.
self.feature_col = feature_col
if self.feature_col >= self.nfields:
raise MissingFieldError( "No field for feature_col (%d)" % feature_col )
self.feature = self.fields[ self.feature_col ]
self.score_col = score_col
if self.score_col >= self.nfields:
raise MissingFieldError( "No field for score_col (%d)" % score_col )
self.score = self.fields[ self.score_col ]
# GFF attributes.
self.attributes = parse_gff_attributes( fields[8] )
def parse_row( self, line ):
# HACK: this should return a GFF interval, but bx-python operations
# require GenomicInterval objects and subclasses will not work.
interval = GenomicInterval( self, line.split( "\t" ), self.chrom_col, self.start_col,
self.end_col, self.strand_col, self.default_strand,
fix_strand=self.fix_strand )
interval = convert_gff_coords_to_bed( interval )
return interval
def complement(reader, lens):
# Handle any ValueError, IndexError and OverflowError exceptions that may be thrown when
# the bitsets are being created by skipping the problem lines
complement_reader = BitsetSafeReaderWrapper(reader, lens=lens)
bitsets = complement_reader.binned_bitsets(upstream_pad=0,
downstream_pad=0,
lens=lens)
# NOT them all
for key, value in bitsets.items():
value.invert()
# Read remaining intervals and subtract
for chrom in bitsets:
bitset = bitsets[chrom]
out_intervals = bits_set_in_range(bitset, 0, lens.get(chrom, MAX))
try:
# Write the intervals
for start, end in out_intervals:
fields = [
"." for x in range(
max(complement_reader.chrom_col, complement_reader.
start_col, complement_reader.end_col) + 1)
]
# default the column to a + if it exists
if complement_reader.strand_col < len(
fields) and complement_reader.strand_col >= 0:
fields[complement_reader.strand_col] = "+"
fields[complement_reader.chrom_col] = chrom
fields[complement_reader.start_col] = start
fields[complement_reader.end_col] = end
new_interval = GenomicInterval(complement_reader, fields,
complement_reader.chrom_col,
complement_reader.start_col,
complement_reader.end_col,
complement_reader.strand_col,
"+")
yield new_interval
except IndexError as e:
complement_reader.skipped += 1
# no reason to stuff an entire bad file into memmory
if complement_reader.skipped < 10:
complement_reader.skipped_lines.append(
(complement_reader.linenum, complement_reader.current_line,
str(e)))
continue
# If "minimum" we output the smallest interval in each cluster
if output == 4 or output == 5:
linenums = list()
f1.seek(0)
fileLines = f1.readlines()
for chrom, tree in clusters.items():
for start, end, lines in tree.getregions():
outsize = -1
outinterval = None
for line in lines:
# three nested for loops?
# should only execute this code once per line
fileline = fileLines[line].rstrip("\n\r")
try:
cluster_interval = GenomicInterval(
g1, fileline.split("\t"), g1.chrom_col,
g1.start_col, g1.end_col, g1.strand_col,
g1.default_strand, g1.fix_strand)
except Exception, exc:
print >> sys.stderr, str(exc)
f1.close()
sys.exit()
interval_size = cluster_interval.end - cluster_interval.start
if outsize == -1 or \
( outsize > interval_size and output == 4 ) or \
( outsize < interval_size and output == 5 ):
outinterval = cluster_interval
outsize = interval_size
out_file.write("%s\n" % outinterval)
f1.close()
out_file.close()
def main():
distance = 0
minregions = 2
output = 1
options, args = doc_optparse.parse(__doc__)
try:
chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg(
options.cols1)
if options.distance:
distance = int(options.distance)
if options.overlap:
distance = -1 * int(options.overlap)
if options.output:
output = int(options.output)
if options.minregions:
minregions = int(options.minregions)
in_fname, out_fname = args
except:
doc_optparse.exception()
g1 = NiceReaderWrapper(fileinput.FileInput(in_fname),
chrom_col=chr_col_1,
start_col=start_col_1,
end_col=end_col_1,
strand_col=strand_col_1,
fix_strand=True)
# Get the cluster tree
try:
clusters, extra = find_clusters(g1,
mincols=distance,
minregions=minregions)
except ParseError as exc:
fail("Invalid file format: %s" % str(exc))
f1 = open(in_fname, "r")
out_file = open(out_fname, "w")
# If "merge"
if output == 1:
fields = [
"."
for x in range(max(g1.chrom_col, g1.start_col, g1.end_col) + 1)
]
for chrom, tree in clusters.items():
for start, end, lines in tree.getregions():
fields[g1.chrom_col] = chrom
fields[g1.start_col] = str(start)
fields[g1.end_col] = str(end)
out_file.write("%s\n" % "\t".join(fields))
# If "filtered" we preserve order of file and comments, etc.
if output == 2:
linenums = dict()
for chrom, tree in clusters.items():
for linenum in tree.getlines():
linenums[linenum] = 0
linenum = -1
f1.seek(0)
for line in f1.readlines():
linenum += 1
if linenum in linenums or linenum in extra:
out_file.write("%s\n" % line.rstrip("\n\r"))
# If "clustered" we output original intervals, but near each other (i.e. clustered)
if output == 3:
linenums = list()
f1.seek(0)
fileLines = f1.readlines()
for chrom, tree in clusters.items():
for linenum in tree.getlines():
out_file.write("%s\n" % fileLines[linenum].rstrip("\n\r"))
# If "minimum" we output the smallest interval in each cluster
if output == 4 or output == 5:
linenums = list()
f1.seek(0)
fileLines = f1.readlines()
for chrom, tree in clusters.items():
for start, end, lines in tree.getregions():
outsize = -1
outinterval = None
for line in lines:
# three nested for loops?
# should only execute this code once per line
fileline = fileLines[line].rstrip("\n\r")
try:
cluster_interval = GenomicInterval(
g1, fileline.split("\t"), g1.chrom_col,
g1.start_col, g1.end_col, g1.strand_col,
g1.default_strand, g1.fix_strand)
except Exception as exc:
print(str(exc), file=sys.stderr)
f1.close()
sys.exit()
interval_size = cluster_interval.end - cluster_interval.start
if outsize == -1 or \
( outsize > interval_size and output == 4 ) or \
( outsize < interval_size and output == 5 ):
outinterval = cluster_interval
outsize = interval_size
out_file.write("%s\n" % outinterval)
f1.close()
out_file.close()
if g1.skipped > 0:
print(skipped(g1, filedesc=""))
