cool-seq-tool 0.8.0__py3-none-any.whl → 0.9.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- cool_seq_tool/mappers/exon_genomic_coords.py +21 -2
- {cool_seq_tool-0.8.0.dist-info → cool_seq_tool-0.9.0.dist-info}/METADATA +31 -31
- {cool_seq_tool-0.8.0.dist-info → cool_seq_tool-0.9.0.dist-info}/RECORD +6 -6
- {cool_seq_tool-0.8.0.dist-info → cool_seq_tool-0.9.0.dist-info}/WHEEL +1 -1
- {cool_seq_tool-0.8.0.dist-info → cool_seq_tool-0.9.0.dist-info}/LICENSE +0 -0
- {cool_seq_tool-0.8.0.dist-info → cool_seq_tool-0.9.0.dist-info}/top_level.txt +0 -0
|
@@ -1169,14 +1169,32 @@ class ExonGenomicCoordsMapper:
|
|
|
1169
1169
|
:param end: Genomic coordinate of breakpoint
|
|
1170
1170
|
:return: Exon number corresponding to adjacent exon. Will be 0-based
|
|
1171
1171
|
"""
|
|
1172
|
-
|
|
1172
|
+
# If a transcript has only one exon, return 0
|
|
1173
|
+
if len(tx_exons_genomic_coords) == 1:
|
|
1174
|
+
return 0
|
|
1175
|
+
|
|
1176
|
+
# Check if a breakpoint occurs before/after the transcript boundaries
|
|
1177
|
+
bp = start if start else end
|
|
1178
|
+
exon_list_len = len(tx_exons_genomic_coords) - 1
|
|
1179
|
+
|
|
1180
|
+
if strand == Strand.POSITIVE:
|
|
1181
|
+
if bp < tx_exons_genomic_coords[0].alt_start_i:
|
|
1182
|
+
return 0
|
|
1183
|
+
if bp > tx_exons_genomic_coords[exon_list_len].alt_end_i:
|
|
1184
|
+
return exon_list_len
|
|
1185
|
+
if strand == Strand.NEGATIVE:
|
|
1186
|
+
if bp > tx_exons_genomic_coords[0].alt_end_i:
|
|
1187
|
+
return 0
|
|
1188
|
+
if bp < tx_exons_genomic_coords[exon_list_len].alt_start_i:
|
|
1189
|
+
return exon_list_len
|
|
1190
|
+
|
|
1191
|
+
for i in range(exon_list_len):
|
|
1173
1192
|
exon = tx_exons_genomic_coords[i]
|
|
1174
1193
|
if start == exon.alt_start_i:
|
|
1175
1194
|
break
|
|
1176
1195
|
if end == exon.alt_end_i:
|
|
1177
1196
|
break
|
|
1178
1197
|
next_exon = tx_exons_genomic_coords[i + 1]
|
|
1179
|
-
bp = start if start else end
|
|
1180
1198
|
if strand == Strand.POSITIVE:
|
|
1181
1199
|
lte_exon = exon
|
|
1182
1200
|
gte_exon = next_exon
|
|
@@ -1185,6 +1203,7 @@ class ExonGenomicCoordsMapper:
|
|
|
1185
1203
|
gte_exon = exon
|
|
1186
1204
|
if bp >= lte_exon.alt_end_i and bp <= gte_exon.alt_start_i:
|
|
1187
1205
|
break
|
|
1206
|
+
|
|
1188
1207
|
# Return current exon if end position is provided, next exon if start position
|
|
1189
1208
|
# is provided.
|
|
1190
1209
|
return exon.ord if end else exon.ord + 1
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
Metadata-Version: 2.1
|
|
2
2
|
Name: cool_seq_tool
|
|
3
|
-
Version: 0.
|
|
3
|
+
Version: 0.9.0
|
|
4
4
|
Summary: Common Operation on Lots of Sequences Tool
|
|
5
5
|
Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
|
|
6
6
|
License: MIT License
|
|
@@ -47,39 +47,39 @@ License-File: LICENSE
|
|
|
47
47
|
Requires-Dist: asyncpg
|
|
48
48
|
Requires-Dist: aiofiles
|
|
49
49
|
Requires-Dist: boto3
|
|
50
|
-
Requires-Dist: agct
|
|
51
|
-
Requires-Dist: polars
|
|
50
|
+
Requires-Dist: agct>=0.1.0-dev1
|
|
51
|
+
Requires-Dist: polars~=1.0
|
|
52
52
|
Requires-Dist: hgvs
|
|
53
53
|
Requires-Dist: biocommons.seqrepo
|
|
54
|
-
Requires-Dist: pydantic
|
|
55
|
-
Requires-Dist: ga4gh.vrs
|
|
56
|
-
Requires-Dist: wags-tails
|
|
54
|
+
Requires-Dist: pydantic==2.*
|
|
55
|
+
Requires-Dist: ga4gh.vrs~=2.0.0a10
|
|
56
|
+
Requires-Dist: wags-tails~=0.2.2
|
|
57
57
|
Requires-Dist: bioutils
|
|
58
58
|
Provides-Extra: dev
|
|
59
|
-
Requires-Dist: pre-commit
|
|
60
|
-
Requires-Dist: ipython
|
|
61
|
-
Requires-Dist: ipykernel
|
|
62
|
-
Requires-Dist: psycopg2-binary
|
|
63
|
-
Requires-Dist: ruff
|
|
59
|
+
Requires-Dist: pre-commit>=3.7.1; extra == "dev"
|
|
60
|
+
Requires-Dist: ipython; extra == "dev"
|
|
61
|
+
Requires-Dist: ipykernel; extra == "dev"
|
|
62
|
+
Requires-Dist: psycopg2-binary; extra == "dev"
|
|
63
|
+
Requires-Dist: ruff==0.5.0; extra == "dev"
|
|
64
|
+
Provides-Extra: tests
|
|
65
|
+
Requires-Dist: pytest; extra == "tests"
|
|
66
|
+
Requires-Dist: pytest-cov; extra == "tests"
|
|
67
|
+
Requires-Dist: pytest-asyncio==0.18.3; extra == "tests"
|
|
68
|
+
Requires-Dist: mock; extra == "tests"
|
|
64
69
|
Provides-Extra: docs
|
|
65
|
-
Requires-Dist: sphinx
|
|
66
|
-
Requires-Dist: sphinx-autodoc-typehints
|
|
67
|
-
Requires-Dist: sphinx-autobuild
|
|
68
|
-
Requires-Dist: sphinx-copybutton
|
|
69
|
-
Requires-Dist: sphinxext-opengraph
|
|
70
|
-
Requires-Dist: furo
|
|
71
|
-
Requires-Dist: sphinx-github-changelog
|
|
72
|
-
Provides-Extra: test
|
|
73
|
-
Requires-Dist: pytest ; extra == 'test'
|
|
74
|
-
Requires-Dist: pytest-cov ; extra == 'test'
|
|
75
|
-
Requires-Dist: pytest-asyncio ==0.18.3 ; extra == 'test'
|
|
76
|
-
Requires-Dist: mock ; extra == 'test'
|
|
70
|
+
Requires-Dist: sphinx==6.1.3; extra == "docs"
|
|
71
|
+
Requires-Dist: sphinx-autodoc-typehints==1.22.0; extra == "docs"
|
|
72
|
+
Requires-Dist: sphinx-autobuild==2021.3.14; extra == "docs"
|
|
73
|
+
Requires-Dist: sphinx-copybutton==0.5.2; extra == "docs"
|
|
74
|
+
Requires-Dist: sphinxext-opengraph==0.8.2; extra == "docs"
|
|
75
|
+
Requires-Dist: furo==2023.3.27; extra == "docs"
|
|
76
|
+
Requires-Dist: sphinx-github-changelog==1.2.1; extra == "docs"
|
|
77
77
|
|
|
78
78
|
<h1 align="center">
|
|
79
|
-
|
|
79
|
+
Cool-Seq-Tool
|
|
80
80
|
</h1>
|
|
81
81
|
|
|
82
|
-
[](https://pypi.python.org/pypi/cool-seq-tool) [](https://pypi.python.org/pypi/cool-seq-tool) [](https://pypi.python.org/pypi/cool-seq-tool) [](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
|
|
82
|
+
[](https://pypi.python.org/pypi/cool-seq-tool) [](https://doi.org/10.5281/zenodo.14007783) [](https://pypi.python.org/pypi/cool-seq-tool) [](https://pypi.python.org/pypi/cool-seq-tool) [](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
|
|
83
83
|
|
|
84
84
|
---
|
|
85
85
|
|
|
@@ -90,18 +90,18 @@ CoolSeqTool
|
|
|
90
90
|
## Overview
|
|
91
91
|
|
|
92
92
|
<!-- description -->
|
|
93
|
-
The **
|
|
93
|
+
The Common Operations On Lots-Of Sequences Tool, **Cool-Seq-Tool**, provides:
|
|
94
94
|
|
|
95
|
-
|
|
96
|
-
|
|
97
|
-
|
|
95
|
+
- A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, [MANE transcript](https://www.ncbi.nlm.nih.gov/refseq/MANE/) descriptions, and transcript alignment data from the [Universal Transcript Archive](https://github.com/biocommons/uta)
|
|
96
|
+
- Augmented access to the [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, including multiple additional methods and tools
|
|
97
|
+
- Mapping tools, including a transcript selection algorithm for selecting a representative transcript defined [here](https://coolseqtool.readthedocs.io/stable/transcript_selection.html), that combine the above to support translation between references sequences, annotation layers, and transcripts
|
|
98
98
|
<!-- /description -->
|
|
99
99
|
|
|
100
100
|
---
|
|
101
101
|
|
|
102
102
|
## Install
|
|
103
103
|
|
|
104
|
-
|
|
104
|
+
Cool-Seq-Tool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
|
|
105
105
|
|
|
106
106
|
```shell
|
|
107
107
|
python3 -m pip install cool-seq-tool
|
|
@@ -113,7 +113,7 @@ See the [installation instructions](https://coolseqtool.readthedocs.io/stable/in
|
|
|
113
113
|
|
|
114
114
|
## Usage
|
|
115
115
|
|
|
116
|
-
All
|
|
116
|
+
All Cool-Seq-Tool resources can be initialized by way of a top-level class instance:
|
|
117
117
|
|
|
118
118
|
```pycon
|
|
119
119
|
>>> from cool_seq_tool import CoolSeqTool
|
|
@@ -6,7 +6,7 @@ cool_seq_tool/handlers/__init__.py,sha256=KalQ46vX1MO4SJz2SlspKoIRy1n3c3Vp1t4Y2p
|
|
|
6
6
|
cool_seq_tool/handlers/seqrepo_access.py,sha256=Jd19jbdUvPRPn_XWozL67ph-nSIxpb4_UUimapDrsm4,9162
|
|
7
7
|
cool_seq_tool/mappers/__init__.py,sha256=O0JRxNFk8nWxD4v5ij47xelhvfVLdEXS43l2tzRuiUE,305
|
|
8
8
|
cool_seq_tool/mappers/alignment.py,sha256=nV6PS3mhkQ2MD1GcpNBujBOqd3AKxYSYA9BCusFOa1o,9636
|
|
9
|
-
cool_seq_tool/mappers/exon_genomic_coords.py,sha256=
|
|
9
|
+
cool_seq_tool/mappers/exon_genomic_coords.py,sha256=XYHWYHL9PcBIKHB_EsN1YKwmhP-KLrGyZv8yH_7huuo,49533
|
|
10
10
|
cool_seq_tool/mappers/liftover.py,sha256=lltx9zxfkrb5PHtJlKp3a39JCwPP4e0Zft-mQc1jXL8,3367
|
|
11
11
|
cool_seq_tool/mappers/mane_transcript.py,sha256=nirxlf3EGVInFYG4fsAqiEmDdTc_h1XuPyX2ul-a7Rk,54368
|
|
12
12
|
cool_seq_tool/resources/__init__.py,sha256=VwUC8YaucTS6SmRirToulZTF6CuvuLQRSxFfSfAovCc,77
|
|
@@ -17,8 +17,8 @@ cool_seq_tool/sources/__init__.py,sha256=51QiymeptF7AeVGgV-tW_9f4pIUr0xtYbyzpvHO
|
|
|
17
17
|
cool_seq_tool/sources/mane_transcript_mappings.py,sha256=Q6J57O2lLWXlgKT0zq3BIwkwFawySnORHOX-UxzfyDE,5399
|
|
18
18
|
cool_seq_tool/sources/transcript_mappings.py,sha256=903RKTMBO2rbKh6iTQ1BEWnY4C7saBFMPw2_4ATuudg,10054
|
|
19
19
|
cool_seq_tool/sources/uta_database.py,sha256=gc5wsKOIhvzhwFmPmqOY0hhaVfRkRSzYNa9tpBt81_U,35017
|
|
20
|
-
cool_seq_tool-0.
|
|
21
|
-
cool_seq_tool-0.
|
|
22
|
-
cool_seq_tool-0.
|
|
23
|
-
cool_seq_tool-0.
|
|
24
|
-
cool_seq_tool-0.
|
|
20
|
+
cool_seq_tool-0.9.0.dist-info/LICENSE,sha256=IpqC9A-tZW7XXXvCS8c4AVINqkmpxiVA-34Qe3CZSjo,1072
|
|
21
|
+
cool_seq_tool-0.9.0.dist-info/METADATA,sha256=GgGZqNTW98YoV49Reizkz2UnPq1MqJOR4jjDHlcWTDQ,6556
|
|
22
|
+
cool_seq_tool-0.9.0.dist-info/WHEEL,sha256=A3WOREP4zgxI0fKrHUG8DC8013e3dK3n7a6HDbcEIwE,91
|
|
23
|
+
cool_seq_tool-0.9.0.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
|
|
24
|
+
cool_seq_tool-0.9.0.dist-info/RECORD,,
|
|
File without changes
|
|
File without changes
|