test: Exhaustive testing

pydeeptools/deeptools/bamCoverage2.py

@@ -143,14 +143,12 @@ def main(args=None):
     if not args.normalizeUsing:
         args.normalizeUsing = 'None'
     if not args.Offset:
+        # no offset is encoded as 0,0
         args.Offset = [0, 0]
-    # in rust, no offset is encoded as 0,0
-    # in python code 1, -1 corresponds to no offset.
     elif len(args.Offset) == 1:
+        # a single offset value is encoded as (value, 0); 0 is otherwise never
         args.Offset = [args.Offset[0], 0]
     else:
-        if args.Offset[1] == -1:
-            args.Offset[1] = 0
         args.Offset = [args.Offset[0], args.Offset[1]]
 
     if not args.extendReads:

pydeeptools/deeptools/computeGCBias.py

@@ -3,6 +3,7 @@
 
 import time
 
+from pathlib import Path
 import multiprocessing
 import numpy as np
 import argparse
@@ -102,7 +103,7 @@ def getRequiredArgs():
                           help='BED file containing genomic regions for which '
                           'extra sampling is required because they are '
                           'underrepresented in the genome.',
-                          type=parserCommon.readableFile,
+                          type=Path,
                           metavar='BED file')
 
     plot = parser.add_argument_group('Diagnostic plot options')

pydeeptools/deeptools/computeMatrix.py

@@ -425,5 +425,5 @@ def main(args=None):
         hm.save_matrix_values(args.outFileNameMatrix)
 
     if args.outFileSortedRegions:
-        with open(args.outFileSortedRegions, 'w') as f:
-            hm.save_BED(f)
+        with open(args.outFileSortedRegions, "w") as fh:
+            hm.save_BED(fh)

pydeeptools/deeptools/computeMatrix2.py

@@ -369,6 +369,7 @@ def computeMatrixOptArgs(case=["scale-regions", "reference-point"][0]):
         "-bl",
         help="A BED file containing regions that should be excluded from all analyses. Currently this works by rejecting genomic chunks that happen to overlap an entry. Consequently, for BAM files, if a read partially overlaps a blacklisted region or a fragment spans over it, then the read/fragment might still be considered.",
         metavar="BED file",
+        default='none',
         required=False,
     )
 
@@ -447,6 +448,8 @@ def process_args(args=None):
         )
     if not args.samplesLabel:
         args.samplesLabel = []
+    else:
+        args.samplesLabel = [i.strip('"').strip("'") for i in args.samplesLabel]
     if not args.sortUsingSamples:
         args.sortUsingSamples = []
 
@@ -461,7 +464,6 @@ def main(args=None):
 
     args = process_args(args)
     signal.signal(signal.SIGINT, signal.SIG_DFL)
-
     sorted_regions_file = args.outFileSortedRegions
 
     r_computematrix(
@@ -476,7 +478,7 @@ def main(args=None):
         args.regionBodyLength,
         args.binSize,
         args.missingDataAsZero,
-        args.keepExons,  # --metagene or not.
+        args.keepExons,
         args.transcriptID,
         args.exonID,
         args.transcript_id_designator,
@@ -485,6 +487,7 @@ def main(args=None):
         args.skipZeros,
         args.minThreshold,
         args.maxThreshold,
+        args.blackListFileName,
         args.averageTypeBins,
         args.sortRegions,
         args.sortUsing,

pydeeptools/deeptools/correctGCBias.py

@@ -6,6 +6,7 @@
 import time
 import subprocess
 import sys
+from pathlib import Path
 
 import py2bit
 import pysam
@@ -91,7 +92,7 @@ def getRequiredArgs():
                           'computeGCBias containing '
                           'the observed and expected read frequencies per GC-'
                           'content.',
-                          type=parserCommon.readableFile,
+                          type=Path,
                           metavar='FILE',
                           required=True)
 

pydeeptools/deeptools/multiBamSummary2.py

@@ -153,15 +153,6 @@ def bamcorrelate_args(case="bins"):
         "after removing the path and extension.",
     )
 
-    optional.add_argument(
-        "--genomeChunkSize",
-        type=int,
-        default=None,
-        help="Manually specify the size of the genome provided to each processor. "
-        "The default value of None specifies that this is determined by read "
-        "density of the BAM file.",
-    )
-
     if case == "bins":
         optional.add_argument(
             "--binSize",

pydeeptools/deeptools/parserCommon.py

@@ -2,7 +2,7 @@
 import os
 from importlib.metadata import version
 import multiprocessing
-
+from pathlib import Path
 
 def check_float_0_1(value):
     v = float(value)
@@ -436,7 +436,7 @@ def heatmapperMatrixArgs(args=None):
     required = parser.add_argument_group('Required arguments')
     required.add_argument('--matrixFile', '-m',
                           help='Matrix file from the computeMatrix tool.',
-                          type=readableFile,
+                          type=Path,
                           )
 
     required.add_argument('--outFileName', '-out', '-o',

pydeeptools/deeptools/plotHeatmap.py

@@ -701,8 +701,8 @@ def main(args=None):
         hm.save_matrix(args.outFileNameMatrix)
 
     if args.outFileSortedRegions:
-        with open(args.outFileSortedRegions, 'w') as f:
-            hm.save_BED(f)
+        with open(args.outFileSortedRegions, "w") as fh:
+            hm.save_BED(fh)
 
     if not args.label_rotation:
         label_rotation=45.0

pydeeptools/deeptools/plotProfile.py

@@ -9,7 +9,7 @@
 from math import ceil
 from deeptools import matplotlib_defaults
 import matplotlib.pyplot as plt
-from matplotlib.font_manager import FontProperties 
+from matplotlib.font_manager import FontProperties
 from matplotlib import colors as pltcolors
 import matplotlib.gridspec as gridspec
 
@@ -76,14 +76,14 @@ def process_args(args=None):
         args.plotHeight = 0.5
     elif args.plotHeight > 100:
         args.plotHeight = 100
-    
+
     if not args.label_rotation:
         args.label_rotation=45.0
     else:
         args.label_rotation= args.label_rotation
-    
+
     if args.ggplot:
-        plt.style.use('ggplot') 
+        plt.style.use('ggplot')
 
     return args
 
@@ -628,8 +628,8 @@ def main(args=None):
                                  averagetype=args.averageType)
 
     if args.outFileSortedRegions:
-        with open(args.outFileSortedRegions, 'w') as f:
-            hm.save_BED(f)
+        with open(args.outFileSortedRegions, "w") as fh:
+            hm.save_BED(fh)
 
     prof = Profile(hm, args.outFileName,
                    plot_title=args.plotTitle,