Merge pull request #109 from lldelisle/smallStuffs

Small stuffs

pygenometracks/readBed.py

@@ -188,7 +188,7 @@ def get_bed_interval(self, bed_line):
                 "not have 8 fields.".format(self.line_number, bed_line)
 
         elif self.file_type == 'bed6':
-            # It is possible that the number of fields was standard.
+            # It is possible that the number of fields was not standard.
             # To be able to process it as bed6, the extra-fields are removed.
             line_data = line_data[:6]
 
@@ -270,6 +270,8 @@ def get_bed_interval(self, bed_line):
             "Start position larger or equal than end" \
             " for line #{}:\n{}\n".format(self.line_number,
                                           bed_line)
+        if len(line_values) == 12:
+            check_bed12(line_values, self.line_number, bed_line)
 
         if len(line_values) < 6:
             assert len(line_values) > 2, \
@@ -285,3 +287,33 @@ def get_bed_interval(self, bed_line):
                            for i in range(6)]
 
         return self.BedInterval._make(line_values)
+
+
+def check_bed12(line_values, line_number, bed_line):
+    block_counts = line_values[9]
+    block_sizes = line_values[10]
+    block_relative_starts = line_values[11]
+    assert len(block_sizes) == block_counts, \
+        "The number of blocks: {} does not correspond to" \
+        "the number of blocks sizes: {}\nline #{}:\n" \
+        "{}".format(block_counts, str(block_sizes),
+                    line_number, bed_line)
+    assert len(block_relative_starts) == block_counts, \
+        "The number of blocks: {} does not correspond to" \
+        "the number of blocks relative starts: {}\nline #{}:\n" \
+        "{}".format(block_counts, str(block_relative_starts),
+                    line_number, bed_line)
+    for i in range(block_counts):
+        block_start = line_values[1] + block_relative_starts[i]
+        block_end = block_start + block_sizes[i]
+        assert block_start <= line_values[2], \
+            "The block number {} of line {} has a starting position " \
+            "greater than the end of the feature:\n{}The" \
+            " 12th field of a bed12 should contains relative start" \
+            " positions of blocks.".format(i, line_number, bed_line)
+        assert block_end <= line_values[2], \
+            "The block number {} of line {} has an ending position " \
+            "greater than the end of the feature:\n{}The" \
+            " 12th field of a bed12 should contains relative start" \
+            " positions of blocks and the 11th field should contains" \
+            " the length of each block.".format(i, line_number, bed_line)

pygenometracks/tests/test_data/narrow_peak.ini

@@ -21,7 +21,7 @@ show labels = no
 color = #0000FF80
 use summit = no
 width adjust = 4
-title = show labels=no;width adjust=3
+title = show labels=no;use summit=no;width adjust=4
 
 [spacer]
 

pygenometracks/tests/test_data/narrow_peak2.ini

@@ -21,7 +21,7 @@ show labels = no
 color = #0000FF80
 use summit = no
 width adjust = 4
-title = show labels=no;width adjust=3
+title = show labels=no;use summit=no;width adjust=4
 
 [spacer]
 

pygenometracks/tests/test_narrowPeakTrack.py

@@ -32,7 +32,7 @@
 color = #0000FF80
 use summit = no
 width adjust = 4
-title = show labels=no;width adjust=3
+title = show labels=no;use summit=no;width adjust=4
 
 [spacer]
 

requirements.txt

@@ -1,7 +1,7 @@
 numpy >=1.16
 matplotlib >=3.0
 intervaltree >=2.1.0
-pybigwig >=0.3.4
+pybigwig >=0.3.16
 future >=0.17.0
 hicmatrix >=9
 pysam >=0.14