From 777c3d7f9ed05c4fd037eb3342bd12e89128ad68 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Tue, 20 Apr 2021 10:33:18 +0200
Subject: [PATCH] Pre-filter intervals before collapsing.
---
bam25prime/__init__.py | 1 +
bam25prime/bam25prime.py | 10 ++++++---
bam25prime/libcollapsebed.pyx | 39 +++++++++++++++++++++++++++++++++++
setup.py | 2 +-
4 files changed, 48 insertions(+), 4 deletions(-)
diff --git a/bam25prime/__init__.py b/bam25prime/__init__.py
index 9ec70ee..f486607 100644
--- a/bam25prime/__init__.py
+++ b/bam25prime/__init__.py
@@ -9,4 +9,5 @@ from .bam25prime import (
collapse_and_sort_bedtool,
filter_feature_size,
make_bed_shifter,
+ make_bed_shift_checker,
)
diff --git a/bam25prime/bam25prime.py b/bam25prime/bam25prime.py
index d57a2fa..c39bacf 100755
--- a/bam25prime/bam25prime.py
+++ b/bam25prime/bam25prime.py
@@ -25,7 +25,9 @@ from pybedtools import BedTool
from pybedtools.featurefuncs import greater_than, less_than
from pysam import AlignmentFile
from .libcollapsesam import collapse_ali
-from .libcollapsebed import collapse_bed, make_bed_shifter
+from .libcollapsebed import (
+ collapse_bed,
+ make_bed_shifter, make_bed_shift_checker)
# pybedtools.Interval | pysam.AlignedSegment
# chrom | reference_name
@@ -94,9 +96,10 @@ def collapse_and_sort(alis, shift=0):
"\n".join(map(collapse_ali, alis)),
from_string=True).sort(stream=True)
shift_bed = make_bed_shifter(shift)
+ canshift_bed = make_bed_shift_checker(shift)
return BedTool(
"\n".join(map(collapse_ali, alis)),
- from_string=True).each(
+ from_string=True).filter(canshift_bed).each(
shift_bed).remove_invalid().sort(stream=True)
@@ -120,7 +123,8 @@ def collapse_and_sort_bedtool(bedtool, shift=0):
if shift == 0:
return bedtool.each(collapse_bed).sort(stream=True)
shift_bed = make_bed_shifter(shift)
- return bedtool.each(collapse_bed).each(
+ canshift_bed = make_bed_shift_checker(shift)
+ return bedtool.each(collapse_bed).filter(canshift_bed).each(
shift_bed).remove_invalid().sort(stream=True)
diff --git a/bam25prime/libcollapsebed.pyx b/bam25prime/libcollapsebed.pyx
index 5266d6c..45a4aaf 100644
--- a/bam25prime/libcollapsebed.pyx
+++ b/bam25prime/libcollapsebed.pyx
@@ -27,6 +27,45 @@ This library contains a cythonized version of a function to collapse
from pybedtools.cbedtools cimport Interval
+cdef ccanshift_bed(Interval bed, int shift):
+ """
+ Check whether the *bed* Interval could be shifted by
+ *shift* positions without having negative coordinates.
+
+ This should be used as filter before attempting shifts,
+ in order to avoid invalid intervals.
+ """
+ if bed.strand == "-":
+ if shift > bed.start):
+ return False
+ # bed.start = bed.start - shift # would be negative
+ # bed.stop = bed.stop - shift
+ else:
+ if (-shift) > bed.start:
+ return False
+ # bed.start = bed.start + shift # would be negative
+ # bed.stop = bed.stop + shift
+ return True
+
+
+def make_bed_shift_checker(shift):
+ """
+ Make a function that checks whether bed intervals
+ can be shifted by *shift* positions (with respect to
+ the feature's orientation).
+ """
+ def canshift_bed(bed):
+ """
+ Check whether the *bed* Interval could be shifted by
+ *shift* positions without having negative coordinates.
+
+ This should be used as filter before attempting shifts,
+ in order to avoid invalid intervals.
+ """
+ return ccanshift_bed(bed, shift)
+ return canshift_bed
+
+
cdef cshift_bed(Interval bed, int shift):
"""
Return the Interval corresponding to the shift
diff --git a/setup.py b/setup.py
index 7bfa7d9..648e71d 100644
--- a/setup.py
+++ b/setup.py
@@ -23,7 +23,7 @@ from pybedtools.helpers import get_includes as pybedtools_get_includes
from pysam import get_include as pysam_get_include
name = "bam25prime"
-__version__ = "0.2"
+__version__ = "0.3"
# https://stackoverflow.com/a/54138355/1878788
--
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