Enable ATAC-seq mode, bump to v0.2.1

jpiper · Nov 25, 2015 · b3def9f · b3def9f
1 parent 5029f59
commit b3def9f
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Showing 4 changed files with 9 additions and 5 deletions.
diff --git a/CHANGES b/CHANGES
@@ -1,3 +1,7 @@
+0.2.1 - 2015-12-25
+==================
+* ENHANCEMENT: ATAC-seq mode for ``wellington_bootstrap.py``
+
 0.2.0 - 2015-12-18
 ==================
 * FEATURE: Differential Footprinting between treatment and control (``wellington_bootstrap.py``)

diff --git a/pyDNase/_version.py b/pyDNase/_version.py
@@ -1 +1 @@
-__version__ = "0.2.0"
+__version__ = "0.2.1"
diff --git a/pyDNase/scripts/wellington_bootstrap.py b/pyDNase/scripts/wellington_bootstrap.py
@@ -157,6 +157,7 @@ def __call__(self):
 parser.add_argument("-p", "--processes", help="Number of processes to use (default: uses all CPUs)",
                     default=0,
                     type=int)
+parser.add_argument("-A", action="store_true", help="ATAC-seq mode (default: False)", default=False)
 parser.add_argument("treatment_bam", help="BAM file for treatment")
 parser.add_argument("control_bam", help="BAM file for control")
 parser.add_argument("bedsites", help="BED file of genomic locations to search in")
@@ -175,9 +176,9 @@ def __call__(self):
 assert args.FDR_limit < 0, "FDR limit must be less than 0"
 
 # Treatment
-reads2 = pyDNase.BAMHandler(args.treatment_bam, caching=0)
+reads2 = pyDNase.BAMHandler(args.treatment_bam, caching=0, ATAC=clargs.A)
 # Control
-reads1 = pyDNase.BAMHandler(args.control_bam, caching=0)
+reads1 = pyDNase.BAMHandler(args.control_bam, caching=0, ATAC=clargs.A)
 # Regions of Interest
 regions = pyDNase.GenomicIntervalSet(args.bedsites)
 # Output

diff --git a/pyDNase/scripts/wellington_footprints.py b/pyDNase/scripts/wellington_footprints.py
@@ -114,7 +114,7 @@ def xrange_from_string(range_string):
 max_regions_cached_in_memory = 10 * CPUs
 p = mp.Pool(CPUs)
 
-#TODO: How about we store a dictionary of open file handles - or would this cause problems with threading?
+
 def writetodisk(fp):
     #Raw WIG scores
     print >> wigout, "fixedStep\tchrom=" + str(fp.interval.chromosome) + "\t start="+ str(fp.interval.startbp) +"\tstep=1"
@@ -147,7 +147,6 @@ def multiWellington(regions,reads,**kwargs):
     p.join()
 
 #TODO: Use **args or something similar to pass arguments?
-#TODO: Pass FDR Iterations, FDR LimiFDR_cutoff=0.01,FDR_iterations=100
 multiWellington(orderedbychr,reads, shoulder_sizes = clargs.shoulder_sizes ,footprint_sizes = clargs.footprint_sizes, FDR_cutoff=clargs.FDR_cutoff,FDR_iterations=clargs.FDR_iterations,bonferroni = clargs.bonferroni)
 
 wigout.close()