cpgtools 2.0.5__py3-none-any.whl

cpgmodule/region2gene.py

@@ -0,0 +1,170 @@
+import sys
+from bx.intervals import *
+import numpy as np
+from cpgmodule import ireader
+
+def getBasalDomains(bedfile, up = 5000, down = 1000, printit = False):
+	'''
+	Define gene's basal regulatory domain. 
+	bedfile: one gene one TSS (could use the canonical (longest) isoform, or merge all isoforms into a super transcript.
+	up: size of extension to upstream of TSS
+	down: size of extension to downstream of TSS
+	'''
+	basal_ranges = {}
+	
+	for l in ireader.reader(bedfile):
+		if l.startswith('#'):
+			continue
+		if l.startswith('track'):
+			continue
+		if l.startswith('browser'):
+			continue
+		f = l.split()
+		try:
+			chrom = f[0]
+			start = int(f[1])
+			end = int(f[2])
+			symbol = f[3]
+			strand = f[5]
+			if start > end:
+				print ("'Start' cannot be larger than 'End'. Skip: " + l, file=sys.stderr)
+				continue		
+		except:
+			print ("BED has at lesat 6 columns. Skip: " + l, file=sys.stderr)
+			continue
+
+		if chrom not in basal_ranges:
+			basal_ranges[chrom] = IntervalTree()
+		
+		if strand == '+':
+			basal_st = (start + 1) - up
+			basal_end = (start + 1) + down
+			basal_st = max(0, basal_st)
+			basal_ranges[chrom].insert_interval( Interval(basal_st, basal_end, strand = '+', value = symbol))
+
+		elif strand == '-':
+			basal_st = end - down
+			basal_end = end + up
+			basal_st = max(0, basal_st)
+			basal_ranges[chrom].insert_interval( Interval(basal_st, basal_end, strand = '-', value = symbol))
+		if printit:
+			print('\t'.join([str(i) for i in (chrom, basal_st, basal_end, symbol, '0', strand)]), file = sys.stdout)
+	return basal_ranges
+
+def geteExtendedDomains(basal_ranges, bedfile, up = 5000, down = 1000, ext=1000000, printit = False):
+	'''
+	Define gene's extended regulatory domain. 
+	bedfile:one gene one TSS (could use the canonical (longest) isoform, or merge all
+			isoforms into a super transcript.
+	ext: 	maximum size of extension (default 1000Kb)
+	
+	Two step process:
+	1) Each gene is assigned a basal regulatory domain of a minimum distance upstream and
+	   downstream of the TSS (regardless of other nearby genes). 
+	2) The gene regulatory domain is extended in both directions to the nearest gene's
+	    basal domain but no more than the maximum extension in one direction.
+	'''	
+	domain_ranges = {}	#gene's regulatory domain range
+	for l in ireader.reader(bedfile):
+		if l.startswith('#'):
+			continue
+		if l.startswith('track'):
+			continue
+		if l.startswith('browser'):
+			continue
+		f = l.split()
+		try:
+			chrom = f[0]
+			start = int(f[1])
+			end = int(f[2])
+			symbol = f[3]
+			strand = f[5]
+			if start > end:
+				print ("'Start' cannot be larger than 'End'. Skip: " + l, file=sys.stderr)
+				continue		
+		except:
+			print ("BED has at lesat 6 columns. Skip: " + l, file=sys.stderr)
+
+		if strand == '+':
+			tss = start + 1
+			basal_st = tss - up
+			basal_end = tss + down
+			extension_st = tss - ext
+			extension_end = tss + ext
+		elif strand == '-':
+			tss = end
+			basal_st = tss - down
+			basal_end = tss + up
+			extension_st = tss - ext
+			extension_end = tss + ext
+		if extension_st < 0: 
+			extension_st = 0
+		#try to update extension_st
+		overlaps = basal_ranges[chrom].find(extension_st, basal_st)
+		if len(overlaps) > 0:
+			for o in overlaps:
+				if o.end > extension_st:
+					extension_st = o.end
+			if extension_st > basal_st:
+				extension_st = basal_st
+
+		#try to update extension_end
+		overlaps = basal_ranges[chrom].find(basal_end, extension_end)
+		if len(overlaps) > 0:
+			for o in overlaps:
+				if o.start < extension_end:
+					extension_end = o.start
+			if extension_end < basal_end:
+				extension_end = basal_end
+								
+		if chrom not in domain_ranges:
+			domain_ranges[chrom] = IntervalTree()
+		else:
+			domain_ranges[chrom].insert_interval(Interval(extension_st, extension_end, strand = strand, value=symbol))
+
+
+		if printit:
+			print('\t'.join([str(i) for i in (chrom, extension_st, extension_end, symbol, '0', strand,  basal_st, basal_end, '255,0,0', 1, extension_end - extension_st, 0)]), file = sys.stdout)
+		
+	return domain_ranges
+	"""
+		if len(overlaps) == 1:
+			domain_ranges[chrom].insert_interval(Interval(extension_st, extension_end, strand = strand, value=symbol))
+			if printit:
+				print('\t'.join([str(i) for i in (chrom, extension_st, extension_end, symbol, '0', strand)]), file = sys.stdout)
+
+		else:
+			o_basal_starts = []	#starts of basal_region overlapped with extension_region
+			o_basal_ends = []
+			for o in overlaps:
+				if o.vallue = symbol:
+					continue
+				o_basal_starts.append(o.start)
+				o_basal_ends.append(o.end)
+			
+			tmp1 = [i for i in o_basal_ends if i > extension_st and i < tss]
+			tmp2 = [i for i in o_basal_starts if i < extension_end and i > tss]
+			if len(tmp1) == 0:
+				truncaed_ext_st = extension_st
+			else:
+				truncaed_ext_st  = max(tmp1)
+			if len(tmp2) == 0:
+				truncaed_ext_end = extension_end
+			else:
+				truncaed_ext_end = min(tmp2)
+			
+			truncaed_ext_st = max(0,truncaed_ext_st)
+			domain_ranges[chrom].insert_interval(Interval(truncaed_ext_st, truncaed_ext_end, strand = strand, value=symbol))
+			
+			if printit:
+				print('\t'.join([str(i) for i in (chrom, truncaed_ext_st, truncaed_ext_end, symbol + '_extended', '0', strand)]), file = sys.stdout)
+	"""
+								
+if __name__=='__main__': 		
+	tmp = basal_domain(sys.argv[1], printit = False)	
+	extended_domain(basal_ranges = tmp, bedfile = sys.argv[1], printit=True)	
+		
+		
+		
+		
+