9781104697

Committed 03 Jul 2024 03:56PM UTC coverage: 88.33% (-6.4%) from 94.753%

Build Type

github

Committed by kodysy02

Commit Message

Defaulting convert_ucsc_contig_names to True for consistency with past behavior

Pull Request Pull Request #253: Defaulting convert_ucsc_contig_names to True for consistency with past behavior

Run Details

1 of 1 new or added line in 1 file covered. (100.0%)

144 existing lines in 17 files now uncovered.

1544 of 1748 relevant lines covered (88.33%)

2.65 hits per line

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58.33

/varcode/effects/transcript_helpers.py

# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.


def interval_offset_on_transcript(start, end, transcript):
    """
    Given an interval [start:end] and a particular transcript,
    return the start offset of the interval relative to the
    chromosomal positions of the transcript.
    """
    # ensure that start_pos:end_pos overlap with transcript positions
    if start > end:
        raise ValueError(
            "start_pos %d shouldn't be greater than end_pos %d" % (
                start, end))
    if start > transcript.end:
        raise ValueError(
            "Range %d:%d starts after transcript %s (%d:%d)" % (
                start,
                end,
                transcript,
                transcript.start,
                transcript.end))
    if end < transcript.start:
        raise ValueError(
            "Range %d:%d ends before transcript %s (%d:%d)" % (
                start,
                end,
                transcript,
                transcript.start,
                transcript.end))
    # trim the start position to the beginning of the transcript
    if start < transcript.start:
        start = transcript.start
    # trim the end position to the end of the transcript
    if end > transcript.end:
        end = transcript.end
    # return earliest offset into the spliced transcript
    return min(
        transcript.spliced_offset(start),
        transcript.spliced_offset(end))

1	# Licensed under the Apache License, Version 2.0 (the "License");
2	# you may not use this file except in compliance with the License.
3	# You may obtain a copy of the License at
4	#
5	# http://www.apache.org/licenses/LICENSE-2.0
6	#
7	# Unless required by applicable law or agreed to in writing, software
8	# distributed under the License is distributed on an "AS IS" BASIS,
9	# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
10	# See the License for the specific language governing permissions and
11	# limitations under the License.
12
13
14	def interval_offset_on_transcript(start, end, transcript):	3✔
15	"""
16	Given an interval [start:end] and a particular transcript,
17	return the start offset of the interval relative to the
18	chromosomal positions of the transcript.
19	"""
20	# ensure that start_pos:end_pos overlap with transcript positions
21	if start > end:	3✔
UNCOV 22	raise ValueError(	×
23	"start_pos %d shouldn't be greater than end_pos %d" % (
24	start, end))
25	if start > transcript.end:	3✔
UNCOV 26	raise ValueError(	×
27	"Range %d:%d starts after transcript %s (%d:%d)" % (
28	start,
29	end,
30	transcript,
31	transcript.start,
32	transcript.end))
33	if end < transcript.start:	3✔
UNCOV 34	raise ValueError(	×
35	"Range %d:%d ends before transcript %s (%d:%d)" % (
36	start,
37	end,
38	transcript,
39	transcript.start,
40	transcript.end))
41	# trim the start position to the beginning of the transcript
42	if start < transcript.start:	3✔
43	start = transcript.start	×
44	# trim the end position to the end of the transcript
45	if end > transcript.end:	3✔
46	end = transcript.end	×
47	# return earliest offset into the spliced transcript
48	return min(	3✔
49	transcript.spliced_offset(start),
50	transcript.spliced_offset(end))

openvax / varcode / 9781104697

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