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From: Michael R. Crusoe <crusoe@debian.org>
Subject: Fix typos
Forwarded: https://github.com/bxlab/bx-python/pull/97
--- a/lib/bx/_seqmapping.pyx
+++ b/lib/bx/_seqmapping.pyx
@@ -187,7 +187,7 @@
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
--- a/lib/bx/align/_epo.pyx
+++ b/lib/bx/align/_epo.pyx
@@ -165,9 +165,9 @@
#@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]
--- a/lib/bx/align/epo.py
+++ b/lib/bx/align/epo.py
@@ -8,7 +8,7 @@
from ._epo import ( # noqa: F401
bed_union,
- cummulative_intervals,
+ cumulative_intervals,
fastLoadChain,
rem_dash,
)
--- a/lib/bx/align/epo_tests.py
+++ b/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 @@
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):
--- a/scripts/bnMapper.py
+++ b/scripts/bnMapper.py
@@ -294,14 +294,14 @@
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
--- a/scripts/maf_tile_2.py
+++ b/scripts/maf_tile_2.py
@@ -185,7 +185,7 @@
# 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
--- a/scripts/maf_tile_2bit.py
+++ b/scripts/maf_tile_2bit.py
@@ -178,7 +178,7 @@
# 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
--- a/scripts/mask_quality.py
+++ b/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
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