Merge pull request #279 from lldelisle/bedgraphAsBigWigUntilNARegion

modify get_scores to reach end_region

pygenometracks/tests/generateAllOutput.sh

@@ -34,6 +34,7 @@ bin/pgt --tracks ./pygenometracks/tests/test_data/bedgraph_useMid.ini --region c
 bin/pgt --tracks ./pygenometracks/tests/test_data/operation_bdg.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o ./pygenometracks/tests/test_data/master_operation_bdg.png
 bin/pgt --tracks ./pygenometracks/tests/test_data/bedgraph_withNA.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o ./pygenometracks/tests/test_data/master_bedgraph_withNA.png
 bin/pgt --tracks ./pygenometracks/tests/test_data/bedgraph_negative.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o ./pygenometracks/tests/test_data/master_negative.png
+bin/pgt --tracks ./pygenometracks/tests/test_data/bedgraph_end_not_covered.ini --region chr7:100-400 --trackLabelFraction 0.2 --dpi 130 -o ./pygenometracks/tests/test_data/master_bedgraph_end_not_covered.png
 
 # test bigWigTrack:
 bin/pgt --tracks ./pygenometracks/tests/test_data/bigwig.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o ./pygenometracks/tests/test_data/master_bigwig.png

pygenometracks/tests/test_bedGraphTrack.py

@@ -214,6 +214,18 @@
 with open(os.path.join(ROOT, "log1pm_bedgraph.ini"), 'w') as fh:
     fh.write(log1p_with_neg)
 
+
+bedgraph_end_not_covered = """
+[bedgraph]
+file = simple.bdg
+height = 3
+summary_method = max
+
+[x-axis]
+"""
+with open(os.path.join(ROOT, "bedgraph_end_not_covered.ini"), 'w') as fh:
+    fh.write(bedgraph_end_not_covered)
+
 tolerance = 13  # default matplotlib pixed difference tolerance
 
 
@@ -427,3 +439,19 @@ def test_bedgraph_neg_log1p():
 
     os.remove(ini_file)
     os.remove(os.path.join(ROOT, "bedgraph_chrx_2e6_5e6_m.bg"))
+
+
+def test_bedgraph_end_not_covered():
+    region = "chr7:100-400"
+    outfile = NamedTemporaryFile(suffix='.png', prefix='bedgraph_end_not_covered_', delete=False)
+    args = "--tracks {ini} --region {region} --trackLabelFraction 0.2 " \
+           "--dpi 130 --outFileName {outfile}" \
+           "".format(ini=os.path.join(ROOT, "bedgraph_end_not_covered.ini"),
+                     outfile=outfile.name, region=region).split()
+    pygenometracks.plotTracks.main(args)
+    print("saving test to {}".format(outfile.name))
+    res = compare_images(os.path.join(ROOT, 'master_bedgraph_end_not_covered.png'),
+                         outfile.name, tolerance)
+    assert res is None, res
+
+    os.remove(outfile.name)

pygenometracks/tests/test_data/bedgraph_end_not_covered.ini

@@ -0,0 +1,7 @@
+
+[bedgraph]
+file = simple.bdg
+height = 3
+summary_method = max
+
+[x-axis]

pygenometracks/tests/test_data/simple.bdg

@@ -0,0 +1,6 @@
+track type=bedGraph name="400-404notIncluded"
+chr7	100	200	1
+chr7	200	300	2
+chr7	300	350	3
+chr7	350	399	4
+chr7	405	450	5

pygenometracks/tracks/BedGraphTrack.py

@@ -229,15 +229,15 @@ def get_scores(self, chrom_region, start_region, end_region,
                    return_nans=True, tbx_var='self.tbx', inttree_var='self.interval_tree'):
         """
         Retrieves the score (or scores or whatever fields are in a bedgraph like file) and the positions
-        for a given region.
+        for a given region. If return_nans is True the pos_list goes until at least end_region.
         In case there is no item in the region. It returns [], []
         Args:
             chrom_region:
             start_region:
             end_region:
         Returns:
             tuple:
-                scores_list, post_list
+                scores_list, pos_list
         """
         score_list = []
         pos_list = []
@@ -288,6 +288,11 @@ def get_scores(self, chrom_region, start_region, end_region,
             score_list.append(values)
             pos_list.append((start, end))
 
+        # Add a last value if needed:
+        if prev_end < end_region and return_nans:
+            score_list.append(np.repeat(np.nan, self.num_fields))
+            pos_list.append((prev_end, end_region))
+
         return score_list, pos_list
 
     def plot(self, ax, chrom_region, start_region, end_region):