def join(leftSet, rightSet, mincols=1, leftfill=True, rightfill=True):
# Read rightSet into memory:
rightlen = 0
leftlen = 0
rightTree = IntervalTree()
for item in rightSet:
if isinstance(item, GenomicInterval):
rightTree.insert( item, rightSet.linenum, item.fields )
if rightlen == 0: rightlen = item.nfields
for interval in leftSet:
if leftlen == 0 and isinstance(interval, GenomicInterval):
leftlen = interval.nfields
if not isinstance(interval, GenomicInterval):
yield interval
else:
result = []
rightTree.intersect( interval, lambda node: result.append( node ) )
overlap_not_met = 0
for item in result:
if item.start in range(interval.start,interval.end+1) and item.end not in range(interval.start,interval.end+1):
overlap = interval.end-item.start
elif item.end in range(interval.start,interval.end+1) and item.start not in range(interval.start,interval.end+1):
overlap = item.end-interval.start
elif item.start in range(interval.start,interval.end+1) and item.end in range(interval.start,interval.end+1):
overlap = item.end-item.start
else: #the intersecting item's start and end are outside the interval range
overlap = interval.end-interval.start
if overlap < mincols:
overlap_not_met += 1
continue
outfields = list(interval)
map(outfields.append, item.other)
setattr( item, "visited", True )
yield outfields
if (len(result) == 0 or overlap_not_met == len(result)) and rightfill:
outfields = list(interval)
for x in range(rightlen): outfields.append(".")
yield outfields
if leftfill:
def report_unvisited( node, results ):
if not hasattr(node, "visited"):
results.append( node )
results = []
rightTree.traverse( lambda x: report_unvisited( x, results ) )
for item in results:
outfields = list()
for x in range(leftlen): outfields.append(".")
map(outfields.append, item.other)
yield outfields
def join(leftSet, rightSet, mincols=1, leftfill=True, rightfill=True):
# Read rightSet into memory:
rightlen = 0
leftlen = 0
rightTree = IntervalTree()
for item in rightSet:
if isinstance(item, GenomicInterval):
rightTree.insert(item, rightSet.linenum, item.fields)
if rightlen == 0: rightlen = item.nfields
for interval in leftSet:
if leftlen == 0 and isinstance(interval, GenomicInterval):
leftlen = interval.nfields
if not isinstance(interval, GenomicInterval):
yield interval
else:
result = []
rightTree.intersect(interval, lambda node: result.append(node))
overlap_not_met = 0
for item in result:
if item.start in range(interval.start, interval.end +
1) and item.end not in range(
interval.start, interval.end + 1):
overlap = interval.end - item.start
elif item.end in range(interval.start, interval.end +
1) and item.start not in range(
interval.start, interval.end + 1):
overlap = item.end - interval.start
elif item.start in range(interval.start, interval.end +
1) and item.end in range(
interval.start, interval.end + 1):
overlap = item.end - item.start
else: #the intersecting item's start and end are outside the interval range
overlap = interval.end - interval.start
if overlap < mincols:
overlap_not_met += 1
continue
outfields = list(interval)
map(outfields.append, item.other)
setattr(item, "visited", True)
yield outfields
if (len(result) == 0
or overlap_not_met == len(result)) and rightfill:
outfields = list(interval)
for x in range(rightlen):
outfields.append(".")
yield outfields
if leftfill:
def report_unvisited(node, results):
if not hasattr(node, "visited"):
results.append(node)
results = []
rightTree.traverse(lambda x: report_unvisited(x, results))
for item in results:
outfields = list()
for x in range(leftlen):
outfields.append(".")
map(outfields.append, item.other)
yield outfields
def join(leftSet, rightSet, mincols=1, leftfill=True, rightfill=True, asfraction=False, matchStrand=STRAND_NEUTRAL, outColumns=[-1,-1]):
# Read rightSet into memory:
rightlen = 0
leftlen = 0
rightStrandCol = -1
minoverlap = mincols
rightTree = IntervalTree()
for item in rightSet:
if isinstance(item, GenomicInterval):
rightTree.insert( item, rightSet.linenum, item.fields )
if rightlen == 0: rightlen = item.nfields
if rightStrandCol == -1: rightStrandCol = item.strand_col
for interval in leftSet:
if leftlen == 0 and isinstance(interval, GenomicInterval):
leftlen = interval.nfields
if not isinstance(interval, GenomicInterval):
yield interval
else:
result = []
rightTree.intersect( interval, lambda node: result.append( node ) )
overlap_not_met = 0
leftbases = interval.end - interval.start
for item in result:
rightbases = item.end - item.start
if (asfraction==True):
if rightbases < leftbases:
mincols = rightbases
else:
mincols = leftbases
mincols = math.floor(mincols * minoverlap)
if item.start in range(interval.start,interval.end+1) and item.end not in range(interval.start,interval.end+1):
overlap = interval.end-item.start
elif item.end in range(interval.start,interval.end+1) and item.start not in range(interval.start,interval.end+1):
overlap = item.end-interval.start
elif item.start in range(interval.start,interval.end+1) and item.end in range(interval.start,interval.end+1):
overlap = item.end-item.start
else: #the intersecting item's start and end are outside the interval range
overlap = interval.end-interval.start
if overlap < mincols:
overlap_not_met += 1
continue
else:
#check strand
strandMatched = STRAND_INTEGER_VALUES[interval.strand] * STRAND_INTEGER_VALUES[item.other[rightStrandCol]]
if (strandMatched == -1 and matchStrand > 0):
#needed match but found a complement
overlap_not_met += 1
continue
if (strandMatched == 1 and matchStrand < 0):
#needed complement but found a match
overlap_not_met += 1
continue
if (strandMatched == 0 and (matchStrand < -1 or matchStrand > 1)):
#strict criteria but only permissive match found
overlap_not_met += 1
continue
#strand criteria met
setattr( item, "visited", True )
yield(getSelectedColumns( interval.fields, item.other, outColumns ))
if (len(result) == 0 or overlap_not_met == len(result)) and rightfill:
yield(getSelectedColumns( interval.fields, rightlen, outColumns ))
if leftfill:
def report_unvisited( node, results ):
if not hasattr(node, "visited"):
results.append( node )
results = []
rightTree.traverse( lambda x: report_unvisited( x, results ) )
for item in results:
yield(getSelectedColumns( leftlen, item.other, outColumns))
def getpairs(leftSet,
rightSet,
leftCol,
mincols=1,
asfraction=False,
matchStrand=STRAND_NEUTRAL,
skipChrNames=True,
skipStrandNames=True):
# Read leftSet into memory:
leftlen = 0
rightlen = 0
leftStrandCol = -1
minoverlap = mincols
leftTree = IntervalTree()
rightCols = list()
for item in leftSet:
if type(item) is GenomicInterval:
leftTree.insert(item, leftSet.linenum, item.fields)
if leftlen == 0: leftlen = item.nfields
if leftStrandCol == -1: leftStrandCol = item.strand_col
for interval in rightSet:
if rightlen == 0 and type(interval) is GenomicInterval:
rightlen = interval.nfields
rightCols = range(rightlen)
#remove the useless columns
rightCols.remove(interval.start_col)
rightCols.remove(interval.end_col)
if skipChrNames:
rightCols.remove(interval.chrom_col)
if skipStrandNames:
rightCols.remove(interval.strand_col)
if not (type(interval) is GenomicInterval):
yield interval
else:
result = []
leftTree.intersect(interval, lambda node: result.append(node))
overlap_not_met = 0
rightbases = interval.end - interval.start
for item in result:
leftbases = item.end - item.start
if (asfraction == True):
if leftbases < rightbases:
mincols = leftbases
else:
mincols = rightbases
mincols = math.floor(mincols * minoverlap)
if (item.start >= interval.start and item.start <= interval.end
) and (item.end < interval.start
or item.end > interval.end):
overlap = interval.end - item.start
elif (item.end >= interval.start and item.end <= interval.end
) and (item.start < interval.start
or item.end > interval.end):
overlap = item.end - interval.start
elif item.start >= interval.start and item.start <= interval.end and item.end >= interval.start and item.end <= interval.end:
overlap = item.end - item.start
else: #the intersecting item's start and end are outside the interval range
overlap = interval.end - interval.start
if overlap < mincols:
overlap_not_met += 1
continue
else:
#check strand
strandMatched = STRAND_INTEGER_VALUES[
interval.strand] * STRAND_INTEGER_VALUES[
item.other[leftStrandCol]]
if (strandMatched == -1 and matchStrand > 0):
#needed match but found a complement
overlap_not_met += 1
continue
if (strandMatched == 1 and matchStrand < 0):
#needed complement but found a match
overlap_not_met += 1
continue
if (strandMatched == 0
and (matchStrand < -1 or matchStrand > 1)):
#strict criteria but only permissive match found
overlap_not_met += 1
continue
#strand criteria met
setattr(item, "visited", True)
leftTerm = item.other[leftCol]
for col in rightCols:
#take each field that's not a number
#split it on semicolons, commas, and spaces
#output the word and the leftTerm as being associated
#curcol = re.sub("\;|\,","\t",interval.fields[col])
curcol = interval.fields[col]
lexer = shlex.shlex(curcol)
lexer.whitespace = '\t\r\n\,\;'
lexer.wordchars += ":'"
lexer.whitespace_split = True
lexer.quotes = '"'
for item in lexer:
item = item.strip()
if (item == "."): continue
try:
float(item)
except ValueError:
yield [item, leftTerm]
def join(
leftSet,
rightSet,
mincols=1,
leftfill=True,
rightfill=True,
asfraction=False,
matchStrand=STRAND_NEUTRAL,
outColumns=[-1, -1],
):
# Read rightSet into memory:
rightlen = 0
leftlen = 0
rightStrandCol = -1
minoverlap = mincols
rightTree = IntervalTree()
for item in rightSet:
if isinstance(item, GenomicInterval):
rightTree.insert(item, rightSet.linenum, item.fields)
if rightlen == 0:
rightlen = item.nfields
if rightStrandCol == -1:
rightStrandCol = item.strand_col
for interval in leftSet:
if leftlen == 0 and isinstance(interval, GenomicInterval):
leftlen = interval.nfields
if not isinstance(interval, GenomicInterval):
yield interval
else:
result = []
rightTree.intersect(interval, lambda node: result.append(node))
overlap_not_met = 0
leftbases = interval.end - interval.start
for item in result:
rightbases = item.end - item.start
if asfraction == True:
if rightbases < leftbases:
mincols = rightbases
else:
mincols = leftbases
mincols = math.floor(mincols * minoverlap)
if item.start in range(interval.start, interval.end + 1) and item.end not in range(
interval.start, interval.end + 1
):
overlap = interval.end - item.start
elif item.end in range(interval.start, interval.end + 1) and item.start not in range(
interval.start, interval.end + 1
):
overlap = item.end - interval.start
elif item.start in range(interval.start, interval.end + 1) and item.end in range(
interval.start, interval.end + 1
):
overlap = item.end - item.start
else: # the intersecting item's start and end are outside the interval range
overlap = interval.end - interval.start
if overlap < mincols:
overlap_not_met += 1
continue
else:
# check strand
strandMatched = (
STRAND_INTEGER_VALUES[interval.strand] * STRAND_INTEGER_VALUES[item.other[rightStrandCol]]
)
if strandMatched == -1 and matchStrand > 0:
# needed match but found a complement
overlap_not_met += 1
continue
if strandMatched == 1 and matchStrand < 0:
# needed complement but found a match
overlap_not_met += 1
continue
if strandMatched == 0 and (matchStrand < -1 or matchStrand > 1):
# strict criteria but only permissive match found
overlap_not_met += 1
continue
# strand criteria met
setattr(item, "visited", True)
yield (getSelectedColumns(interval.fields, item.other, outColumns))
if (len(result) == 0 or overlap_not_met == len(result)) and rightfill:
yield (getSelectedColumns(interval.fields, rightlen, outColumns))
if leftfill:
def report_unvisited(node, results):
if not hasattr(node, "visited"):
results.append(node)
results = []
rightTree.traverse(lambda x: report_unvisited(x, results))
for item in results:
yield (getSelectedColumns(leftlen, item.other, outColumns))
def getpairs(leftSet, rightSet, leftCol, mincols=1, asfraction=False, matchStrand=STRAND_NEUTRAL, skipChrNames=True, skipStrandNames=True):
# Read leftSet into memory:
leftlen = 0
rightlen = 0
leftStrandCol = -1
minoverlap = mincols
leftTree = IntervalTree()
rightCols = list()
for item in leftSet:
if type( item ) is GenomicInterval:
leftTree.insert( item, leftSet.linenum, item.fields )
if leftlen == 0: leftlen = item.nfields
if leftStrandCol == -1: leftStrandCol = item.strand_col
for interval in rightSet:
if rightlen == 0 and type( interval ) is GenomicInterval:
rightlen = interval.nfields
rightCols = range(rightlen)
#remove the useless columns
rightCols.remove( interval.start_col )
rightCols.remove( interval.end_col )
if skipChrNames:
rightCols.remove( interval.chrom_col )
if skipStrandNames:
rightCols.remove( interval.strand_col )
if not (type( interval ) is GenomicInterval):
yield interval
else:
result = []
leftTree.intersect( interval, lambda node: result.append( node ) )
overlap_not_met = 0
rightbases = interval.end - interval.start
for item in result:
leftbases = item.end - item.start
if (asfraction==True):
if leftbases < rightbases:
mincols = leftbases
else:
mincols = rightbases
mincols = math.floor(mincols * minoverlap)
if (item.start >= interval.start and item.start <= interval.end) and (item.end < interval.start or item.end > interval.end):
overlap = interval.end-item.start
elif (item.end >= interval.start and item.end <= interval.end) and (item.start < interval.start or item.end > interval.end):
overlap = item.end-interval.start
elif item.start >= interval.start and item.start <= interval.end and item.end >= interval.start and item.end <= interval.end:
overlap = item.end-item.start
else: #the intersecting item's start and end are outside the interval range
overlap = interval.end-interval.start
if overlap < mincols:
overlap_not_met += 1
continue
else:
#check strand
strandMatched = STRAND_INTEGER_VALUES[interval.strand] * STRAND_INTEGER_VALUES[item.other[leftStrandCol]]
if (strandMatched == -1 and matchStrand > 0):
#needed match but found a complement
overlap_not_met += 1
continue
if (strandMatched == 1 and matchStrand < 0):
#needed complement but found a match
overlap_not_met += 1
continue
if (strandMatched == 0 and (matchStrand < -1 or matchStrand > 1)):
#strict criteria but only permissive match found
overlap_not_met += 1
continue
#strand criteria met
setattr( item, "visited", True )
leftTerm = item.other[leftCol]
for col in rightCols:
#take each field that's not a number
#split it on semicolons, commas, and spaces
#output the word and the leftTerm as being associated
#curcol = re.sub("\;|\,","\t",interval.fields[col])
curcol= interval.fields[col]
lexer = shlex.shlex(curcol)
lexer.whitespace='\t\r\n\,\;'
lexer.wordchars += ":'"
lexer.whitespace_split=True
lexer.quotes='"'
for item in lexer:
item = item.strip()
if (item == "."): continue
try:
float(item)
except ValueError:
yield [item, leftTerm]
