Merge branch 'master' into network

CHANGES

@@ -1,3 +1,6 @@
+## 0.6.4 (2019-08-07)
+- Bug fix for error with regions very close to chromosome borders for ATACorrect and ScoreBigwig. 
+
 ## 0.6.3 (2019-07-16)
 - Increased size of texts in BINDetect volcano plot and moved label into plot
 

tobias/__init__.py

@@ -1 +1 @@
-__version__ = "0.6.3"
+__version__ = "0.6.4"

tobias/footprinting/atacorrect.py

@@ -235,10 +235,13 @@ def run_atacorrect(args):
 		output_regions = RegionList().from_bed(args.regions_out)
 	else:
 		output_regions = deepcopy(peak_regions)
-
-	output_regions.apply_method(OneRegion.extend_reg, args.extend)
+
+	#Extend regions to make sure extend + flanking for window/flank are within boundaries
+	flank_extend = args.k_flank + int(args.window/2.0)
+	output_regions.apply_method(OneRegion.extend_reg, args.extend + flank_extend)
 	output_regions.merge()	
 	output_regions.apply_method(OneRegion.check_boundary, bam_chrom_info, "cut")
+	output_regions.apply_method(OneRegion.extend_reg, -flank_extend)	#Cut to needed size knowing that the region will be extended in function
 
 	#Remove blacklisted regions and chromosomes not in common
 	blacklist_regions = RegionList().from_bed(args.blacklist) if args.blacklist != None else RegionList([])	 #fill in with regions from args.blacklist

tobias/footprinting/atacorrect_functions.py

@@ -194,7 +194,7 @@ def bias_correction(regions_list, params, bias_obj):
 	for region_obj in regions_list:
 
 		region_obj.extend_reg(f_extend)
-		region_obj.check_boundary(chrom_lengths, "cut")
+		#region_obj.check_boundary(chrom_lengths, "cut")	#moved to outside of function
 		reg_len = region_obj.get_length()	#length including flanking
 		reg_key = (region_obj.chrom, region_obj.start+f_extend, region_obj.end-f_extend)	#output region
 		out_signals[reg_key] = {"uncorrected":{}, "bias":{}, "expected":{}, "corrected":{}}

tobias/footprinting/scorebigwig.py

@@ -74,6 +74,8 @@ def add_scorebigwig_arguments(parser):
 #------------------------------------------------------------------#
 def calculate_scores(regions, args):
 
+	logger = TobiasLogger("", args.verbosity, args.log_q)
+
 	pybw_signal = pyBigWig.open(args.signal) 	#cutsites signal
 	pybw_header = pybw_signal.chroms()			
 	chrom_lengths = {chrom:int(pybw_header[chrom]) for chrom in pybw_header}
@@ -84,6 +86,8 @@ def calculate_scores(regions, args):
 	#Go through each region
 	for i, region in enumerate(regions):
 
+		logger.debug("Calculating scores for region: {0}".format(region))
+
 		#Extend region with necessary flank
 		region.extend_reg(flank)
 		reg_key = (region.chrom, region.start+flank, region.end-flank)	#output region
@@ -168,14 +172,16 @@ def run_scorebigwig(args):
 	pybw_signal = pyBigWig.open(args.signal)
 	pybw_header = pybw_signal.chroms()
 	chrom_info = {chrom:int(pybw_header[chrom]) for chrom in pybw_header}
+	logger.debug("Chromosome lengths from input bigwig: {0}".format(chrom_info))
 
 	#Decide regions 
 	logger.info("- Getting output regions ready")
 	if args.regions:
 		regions = RegionList().from_bed(args.regions)
 		regions.apply_method(OneRegion.extend_reg, args.extend)
 		regions.merge()
-		regions.apply_method(OneRegion.check_boundary, chrom_info)
+		regions.apply_method(OneRegion.check_boundary, chrom_info, "cut")
+
 	else:
 		regions = RegionList().from_list([OneRegion([chrom, 0, chrom_info[chrom]]) for chrom in chrom_info])	
 
@@ -190,9 +196,8 @@ def run_scorebigwig(args):
 	#Go through each region
 	for i, region in enumerate(regions):
 		region.extend_reg(args.region_flank)
-		region.check_boundary(chrom_info, "cut")	
-		region.start = region.start + args.region_flank
-		region.end = region.end - args.region_flank
+		region = region.check_boundary(chrom_info, "cut")
+		region.extend_reg(-args.region_flank)
 
 	#Information for output bigwig
 	reference_chroms = sorted(list(chrom_info.keys()))

tobias/utils/regions.py

@@ -139,6 +139,9 @@ def check_boundary(self, boundaries_dict, action="cut"):
 		else:
 			exit("Error in regions.check_boundary: unknown action")
 
+		self[1] = self.start
+		self[2] = self.end
+
 		return(self)
 
 	def get_signal(self, pybw, numpy_bool = True):

tobias/utils/utilities.py

@@ -168,6 +168,7 @@ def bigwig_writer(q, key_file_dict, header, regions, args):
 					if i_to_write[akey] != no_regions - 1:
 						logger.error("Wrote {0} regions but there are {1} in total".format(i_to_write[akey], len(region_tups)))
 						logger.error("Ready_to_write[{0}]: {1}".format(akey, len(ready_to_write[akey])))
+						sys.exit()
 				break
 
 			#Save key:region:signal to ready_to_write