Fix typos

lib/bx/_seqmapping.pyx

@@ -166,7 +166,7 @@ cdef class IntToIntMapping:
         return copy
 
     def expand( self, int x ):
-        """Grow the alphabet by making 'a' a seperate symbol. If it already mapped to a single symbol, do nothing"""
+        """Grow the alphabet by making 'a' a separate symbol. If it already mapped to a single symbol, do nothing"""
         cdef int i, count, a, b
         cdef IntToIntMapping copy
         # Get the symbol x maps to

lib/bx/align/_epo.pyx

@@ -165,9 +165,9 @@ cpdef numpy.ndarray[numpy.uint64_t, ndim=2] bed_union( numpy.ndarray[numpy.uint6
 
 #@cython.wraparound(False)
 #@cython.boundscheck(False)
-cpdef numpy.ndarray[numpy.int64_t, ndim=2] cummulative_intervals(numpy.ndarray[numpy.int64_t, ndim=1] S,
+cpdef numpy.ndarray[numpy.int64_t, ndim=2] cumulative_intervals(numpy.ndarray[numpy.int64_t, ndim=1] S,
         numpy.ndarray[numpy.int64_t, ndim=1] D ):
-    """compute cummulative intervals for this side of an aligmnent. S and D are one side of
+    """compute cumulative intervals for this side of an aligmnent. S and D are one side of
     the alignment as described in the chain file format"""
 
     cdef int N = S.shape[0]

lib/bx/align/epo.py

@@ -8,7 +8,7 @@
 
 from ._epo import (  # noqa: F401
     bed_union,
-    cummulative_intervals,
+    cumulative_intervals,
     fastLoadChain,
     rem_dash,
 )

lib/bx/align/epo_tests.py

@@ -8,7 +8,7 @@
 
 from bx.align._epo import (
     bed_union,
-    cummulative_intervals,
+    cumulative_intervals,
 )
 from bx.align.epo import (
     Chain,
@@ -26,7 +26,7 @@ def test_ci(self):
             S.append(random.randint(10, 50))
             D.append(random.randint(10, 50))
         D[-1] = 0
-        C = cummulative_intervals(np.array(S, dtype=np.int64), np.array(D, dtype=np.int64))
+        C = cumulative_intervals(np.array(S, dtype=np.int64), np.array(D, dtype=np.int64))
         for i in range(self.N):
             assert C[i, 1] - C[i, 0] == S[i]
         for i in range(1, self.N):

scripts/bnMapper.py

@@ -292,14 +292,14 @@ def loadChains(path):
 
     EPO = epo.Chain._parse_file(path, True)
     # convert coordinates w.r.t the forward strand (into slices)
-    # compute cummulative intervals
+    # compute cumulative intervals
     for i in range(len(EPO)):
         ch, S, T, Q = EPO[i]
         if ch.tStrand == "-":
             ch = ch._replace(tEnd=ch.tSize - ch.tStart, tStart=ch.tSize - ch.tEnd)
         if ch.qStrand == "-":
             ch = ch._replace(qEnd=ch.qSize - ch.qStart, qStart=ch.qSize - ch.qEnd)
-        EPO[i] = (ch, epo.cummulative_intervals(S, T), epo.cummulative_intervals(S, Q))
+        EPO[i] = (ch, epo.cumulative_intervals(S, T), epo.cumulative_intervals(S, Q))
     # now each element of epo is (chain_header, target_intervals, query_intervals)
     assert all(t[0].tStrand == "+" for t in EPO), "all target strands should be +"
     return EPO

scripts/maf_tile_2.py

@@ -186,7 +186,7 @@ def do_interval(sources, index, out, ref_src, start, end, seq_db, missing_data,
         # Store the size of the reference sequence for building fake block
         if ref_src_size is None:
             ref_src_size = ref.src_size
-        # Handle the reference component seperately, it has no synteny status
+        # Handle the reference component separately, it has no synteny status
         # but we will try to fill in missing sequence
         if ref.start > last_stop:
             # Need to fill in some reference sequence

scripts/maf_tile_2bit.py

@@ -178,7 +178,7 @@ def do_interval(sources, index, out, ref_src, start, end, ref_2bit, missing_data
         # Store the size of the reference sequence for building fake block
         if ref_src_size is None:
             ref_src_size = ref.src_size
-        # Handle the reference component seperately, it has no synteny status
+        # Handle the reference component separately, it has no synteny status
         # but we will try to fill in missing sequence
         if ref.start > last_stop:
             # Need to fill in some reference sequence

scripts/mask_quality.py

@@ -12,7 +12,7 @@
     -m, --mask=N: Character to use as mask character
     -q, --quality=N: Min quality allowed
     -t, --type=N: base_pair or nqs
-    -l, --list=N: colon seperated list of species,len_file[,qualityfile].
+    -l, --list=N: colon separated list of species,len_file[,qualityfile].
 """
 
 import fileinput