v0.6.5 bump

NEWS

@@ -1,4 +1,8 @@
 
+# 0.6.5
+- Fix an error in bap-barcode as well as warning reporting
+- Auto-remove whitespace from the genome parser
+
 # 0.6.4
 - Inclusion of a prior table to skip merges when a prior annotation is known
 

bap/bap2ProjectClass.py

@@ -161,7 +161,6 @@ def __init__(self, script_dir, supported_genomes, mode, input, output, name, nco
 		#------------------------
 		self.reference_genome = reference_genome
 		if any(self.reference_genome == s for s in supported_genomes):
-			click.echo(gettime() + "Found designated reference genome: %s" % self.reference_genome)
 
 			self.tssFile = script_dir + "/anno/TSS/" + self.reference_genome + ".refGene.TSS.bed"
 			self.blacklistFile = script_dir + "/anno/blacklist/" + self.reference_genome + ".full.blacklist.bed"
@@ -187,9 +186,14 @@ def __init__(self, script_dir, supported_genomes, mode, input, output, name, nco
 		#------------------------------	
 		if(bedtools_genome != ""):
 			if(os.path.isfile(bedtools_genome)):
+				click.echo(gettime() + "Importing custom reference genome files.")
 				self.bedtoolsGenomeFile = bedtools_genome
 			else: 
 				sys.exit("Could not find the bedtools genome file: %s" % bedtools_genome)
+		else:
+			# Cleaned up case
+			click.echo(gettime() + "Found designated reference genome: %s" % self.reference_genome)
+
 
 		if(blacklist_file != ""):
 			if(os.path.isfile(blacklist_file)):
@@ -207,7 +211,7 @@ def __init__(self, script_dir, supported_genomes, mode, input, output, name, nco
 			if(os.path.isfile(peak_file)):
 				self.peakFile = peak_file
 			else: 
-				sys.exit("Could not find the transcription start sites file: %s" % peak_file)
+				sys.exit("Could not find the peaks file: %s" % peak_file)
 		else:
 			self.peakFile = ""
 

bap/barcode/cli_barcode.py

@@ -44,7 +44,7 @@ def main(mode, fastq1, fastq2, fastqi, output, ncores, nreads, nmismatches, reve
 
 	__version__ = get_distribution('bap-atac').version
 	script_dir = os.path.dirname(os.path.realpath(__file__))
-	click.echo(gettime() + "Starting de-barcoding from bap pipeline v%s" % __version__)
+	click.echo(gettime() + "Starting de-barcoding from bap pipeline v%s\n" % __version__)
 
 	# Parse user settings
 	core_call1 = " --fastq1 " + fastq1 + " --fastq2 " + fastq2 + " --ncores " + str(ncores) 
@@ -80,6 +80,6 @@ def main(mode, fastq1, fastq2, fastqi, output, ncores, nreads, nmismatches, reve
 		sys.exit(gettime() + "User-supplied mode %s not found!" % mode)
 
 	# Assemble the final call
-	sys_call = cmd + earlier + later + core_call
+	sys_call = cmd + earlier + later + core_call + " 2> "+output+".stderr.txt"
 	os.system(sys_call)
 

bap/cli_bap2.py

@@ -151,7 +151,8 @@ def main(mode, input, output, name, ncores, reference_genome,
 		chrs_ref = []
 		with open(p.bedtoolsGenomeFile) as f:
 			for line in f:
-				chrs_ref.append(line.split("\t")[0])
+				if line.rstrip():
+					chrs_ref.append(line.split("\t")[0])
 
 		# Quant the overlaps and exit if no overlap
 		chrs_both = intersection(chrs_bam, chrs_ref)

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name='bap-atac',
-    version='0.6.4a',
+    version='0.6.5',
     url='https://github.com/caleblareau/bap',
     license='MIT',
     author='Caleb Lareau',

tests/README.md

@@ -24,6 +24,10 @@ time bap2 bam -i data/small_mix.bam -bt XB -ji 0.0001 -r hg19-mm10 -z --mapq 0 -
 time bap2 bam -i data/jaccardPairsForIGV.bam -bt XB -r hg19 -z -o bap2 -pf data/test.small.peaks.bed -bp data/jaccardPairsTest_sep.tsv 
 ```
 
+```
+bap-barcode v2.1 -a fastq_br/biorad_v2_R1.fastq.gz -b fastq_br/biorad_v2_R2.fastq.gz -o test
+```
+
 
 #### Docker