cool-seq-tool 0.4.0.dev1__py3-none-any.whl → 0.4.0.dev2__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/data/__init__.py +1 -1
- cool_seq_tool/data/data_downloads.py +19 -13
- cool_seq_tool/handlers/seqrepo_access.py +2 -4
- cool_seq_tool/mappers/exon_genomic_coords.py +25 -26
- cool_seq_tool/mappers/mane_transcript.py +112 -106
- cool_seq_tool/routers/default.py +7 -9
- cool_seq_tool/routers/mane.py +2 -2
- cool_seq_tool/schemas.py +30 -21
- cool_seq_tool/sources/mane_transcript_mappings.py +1 -1
- cool_seq_tool/sources/transcript_mappings.py +13 -16
- cool_seq_tool/sources/uta_database.py +134 -153
- cool_seq_tool/utils.py +5 -2
- cool_seq_tool/version.py +1 -1
- {cool_seq_tool-0.4.0.dev1.dist-info → cool_seq_tool-0.4.0.dev2.dist-info}/METADATA +7 -6
- cool_seq_tool-0.4.0.dev2.dist-info/RECORD +29 -0
- cool_seq_tool-0.4.0.dev1.dist-info/RECORD +0 -29
- {cool_seq_tool-0.4.0.dev1.dist-info → cool_seq_tool-0.4.0.dev2.dist-info}/LICENSE +0 -0
- {cool_seq_tool-0.4.0.dev1.dist-info → cool_seq_tool-0.4.0.dev2.dist-info}/WHEEL +0 -0
- {cool_seq_tool-0.4.0.dev1.dist-info → cool_seq_tool-0.4.0.dev2.dist-info}/top_level.txt +0 -0
@@ -1,6 +1,6 @@
|
|
1
1
|
Metadata-Version: 2.1
|
2
2
|
Name: cool_seq_tool
|
3
|
-
Version: 0.4.0.
|
3
|
+
Version: 0.4.0.dev2
|
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
|
@@ -49,7 +49,7 @@ License-File: LICENSE
|
|
49
49
|
Requires-Dist: asyncpg
|
50
50
|
Requires-Dist: aiofiles
|
51
51
|
Requires-Dist: boto3
|
52
|
-
Requires-Dist:
|
52
|
+
Requires-Dist: agct >=0.1.0-dev1
|
53
53
|
Requires-Dist: polars
|
54
54
|
Requires-Dist: hgvs
|
55
55
|
Requires-Dist: biocommons.seqrepo
|
@@ -62,7 +62,7 @@ Requires-Dist: pre-commit ; extra == 'dev'
|
|
62
62
|
Requires-Dist: ipython ; extra == 'dev'
|
63
63
|
Requires-Dist: ipykernel ; extra == 'dev'
|
64
64
|
Requires-Dist: psycopg2-binary ; extra == 'dev'
|
65
|
-
Requires-Dist: ruff ; extra == 'dev'
|
65
|
+
Requires-Dist: ruff >=0.1.14 ; extra == 'dev'
|
66
66
|
Provides-Extra: docs
|
67
67
|
Requires-Dist: sphinx ==6.1.3 ; extra == 'docs'
|
68
68
|
Requires-Dist: sphinx-autodoc-typehints ==1.22.0 ; extra == 'docs'
|
@@ -70,6 +70,7 @@ Requires-Dist: sphinx-autobuild ==2021.3.14 ; extra == 'docs'
|
|
70
70
|
Requires-Dist: sphinx-copybutton ==0.5.2 ; extra == 'docs'
|
71
71
|
Requires-Dist: sphinxext-opengraph ==0.8.2 ; extra == 'docs'
|
72
72
|
Requires-Dist: furo ==2023.3.27 ; extra == 'docs'
|
73
|
+
Requires-Dist: sphinx-github-changelog ==1.2.1 ; extra == 'docs'
|
73
74
|
Provides-Extra: tests
|
74
75
|
Requires-Dist: pytest ; extra == 'tests'
|
75
76
|
Requires-Dist: pytest-cov ; extra == 'tests'
|
@@ -80,7 +81,7 @@ Requires-Dist: mock ; extra == 'tests'
|
|
80
81
|
CoolSeqTool
|
81
82
|
</h1>
|
82
83
|
|
83
|
-
**[Documentation](https://coolseqtool.readthedocs.io/
|
84
|
+
**[Documentation](https://coolseqtool.readthedocs.io/latest/)** · [Installation](https://coolseqtool.readthedocs.io/latest/install.html) · [Usage](https://coolseqtool.readthedocs.io/latest/usage.html) · [API reference](https://coolseqtool.readthedocs.io/latest/reference/index.html)
|
84
85
|
|
85
86
|
## Overview
|
86
87
|
|
@@ -102,7 +103,7 @@ CoolSeqTool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
|
|
102
103
|
python3 -m pip install cool-seq-tool
|
103
104
|
```
|
104
105
|
|
105
|
-
See the [installation instructions](https://coolseqtool.readthedocs.io/
|
106
|
+
See the [installation instructions](https://coolseqtool.readthedocs.io/latest/install.html) in the documentation for a description of dependency setup requirements.
|
106
107
|
|
107
108
|
---
|
108
109
|
|
@@ -127,4 +128,4 @@ All CoolSeqTool resources can be initialized by way of a top-level class instanc
|
|
127
128
|
|
128
129
|
## Feedback and contributing
|
129
130
|
|
130
|
-
We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The [documentation](https://coolseqtool.readthedocs.io/
|
131
|
+
We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The [documentation](https://coolseqtool.readthedocs.io/latest/contributing.html) contains guidance for submitting feedback and contributing new code.
|
@@ -0,0 +1,29 @@
|
|
1
|
+
cool_seq_tool/__init__.py,sha256=eBycAZIAJBCf51xQLQYHzvUep1i21LMrzBdRLqfe-Fc,352
|
2
|
+
cool_seq_tool/api.py,sha256=3Pc0j0pHMZ_3skTkjDlQpcu_MM6kyNPmBrwm_LrH-rw,1234
|
3
|
+
cool_seq_tool/app.py,sha256=3r2hlajW6xjf3u_Uf9WlqMfBEK-LnB74sG2UpJlj2bY,3757
|
4
|
+
cool_seq_tool/paths.py,sha256=7EA21Vmf9hvct0z_V4oK0WTWOA2FKY2Tavh4nAUXunk,889
|
5
|
+
cool_seq_tool/schemas.py,sha256=Uw5OkC0dPM_RC8ZHNn1wLZBZK_kWAkkQQRrh-zOsJjg,15922
|
6
|
+
cool_seq_tool/utils.py,sha256=26y_25V029l-ra3We3z-KQFfgRlcvfl2dQ8XJ1t6yfM,1625
|
7
|
+
cool_seq_tool/version.py,sha256=cuIT6sKXUqxwO7uw5ifUO0f7jv19ApxBFZMLy2jwNgo,57
|
8
|
+
cool_seq_tool/data/__init__.py,sha256=pOdws59_iPOP0V4xqx55PdxCUxHSA5N_Eo5L0oZsafs,63
|
9
|
+
cool_seq_tool/data/data_downloads.py,sha256=WaTxeCnifBuif89_lo6hFrmTu2gu8Jy8ndB9crcqvFQ,3869
|
10
|
+
cool_seq_tool/data/transcript_mapping.tsv,sha256=AO3luYQAbFiCoRgiiPXotakb5pAwx1jDCeXpvGdIuac,24138769
|
11
|
+
cool_seq_tool/handlers/__init__.py,sha256=xDQ84N4ImrUBKwGmrg64yGUMh0ArW-DwjJuTkKrIJL4,77
|
12
|
+
cool_seq_tool/handlers/seqrepo_access.py,sha256=XUS4zjguXB7OfLZLnQatWwiYVspu87rk50v1WzENvXE,9029
|
13
|
+
cool_seq_tool/mappers/__init__.py,sha256=5aE6IRTG8SwOofFR19QHmK-1n2PaKwEPzFGNE0_HS3s,261
|
14
|
+
cool_seq_tool/mappers/alignment.py,sha256=htGb9rJab8dAKcMR62NF0uGc5l4KROrMcMAKfSQhva0,9620
|
15
|
+
cool_seq_tool/mappers/exon_genomic_coords.py,sha256=vuU1vtEzgwGqGFywDOEia8I-46qsAhRI1fM_PkbpBnk,30809
|
16
|
+
cool_seq_tool/mappers/mane_transcript.py,sha256=XB51pcR5TCtteXS525NgP2S7aRU1gnBtB2ZrSltxM1A,49364
|
17
|
+
cool_seq_tool/routers/__init__.py,sha256=x00Dq0LzqYoBPbipmyexLbAMUb7Udx8DozfwT-mJo1E,436
|
18
|
+
cool_seq_tool/routers/default.py,sha256=nMDcAAdo-QZugs6k43HnYJCzhorg9nFt0TsdXTckVZU,3927
|
19
|
+
cool_seq_tool/routers/mane.py,sha256=fASm7wo4ZjYB5l8G5cu4zqObwf811SxLVCJhbeqC_cY,3544
|
20
|
+
cool_seq_tool/routers/mappings.py,sha256=I9hxriBlkv9vQp1l_17L-VxQSUJ9-IyLyqwXGue4axg,6091
|
21
|
+
cool_seq_tool/sources/__init__.py,sha256=lERBM8cOqlJhYqz_DwOMV5FsWvMvQMbU1KQBxx_cz6M,303
|
22
|
+
cool_seq_tool/sources/mane_transcript_mappings.py,sha256=Oyq7cdUJ2j0isROCkHW-rgtU7LtyFon3DJz6hrEl5cU,3750
|
23
|
+
cool_seq_tool/sources/transcript_mappings.py,sha256=_CV71tyge24rr7Kb_rJJQTr9uG1lSU_O-HcC9hIc5OQ,9731
|
24
|
+
cool_seq_tool/sources/uta_database.py,sha256=nlvEIsdZxY7z4-PfTWVbpt5O4fMNgHWHmFxx3lL-mgM,43578
|
25
|
+
cool_seq_tool-0.4.0.dev2.dist-info/LICENSE,sha256=1jbnPcw_qmlDZyD_E_ebjWwjIvBgOD-1biodvBtSl1U,1072
|
26
|
+
cool_seq_tool-0.4.0.dev2.dist-info/METADATA,sha256=adcWEq-_TLdFRhIfnDmVPyu4i_xMM9uXA9qWN5mZNq0,5721
|
27
|
+
cool_seq_tool-0.4.0.dev2.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
|
28
|
+
cool_seq_tool-0.4.0.dev2.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
|
29
|
+
cool_seq_tool-0.4.0.dev2.dist-info/RECORD,,
|
@@ -1,29 +0,0 @@
|
|
1
|
-
cool_seq_tool/__init__.py,sha256=eBycAZIAJBCf51xQLQYHzvUep1i21LMrzBdRLqfe-Fc,352
|
2
|
-
cool_seq_tool/api.py,sha256=3Pc0j0pHMZ_3skTkjDlQpcu_MM6kyNPmBrwm_LrH-rw,1234
|
3
|
-
cool_seq_tool/app.py,sha256=3r2hlajW6xjf3u_Uf9WlqMfBEK-LnB74sG2UpJlj2bY,3757
|
4
|
-
cool_seq_tool/paths.py,sha256=7EA21Vmf9hvct0z_V4oK0WTWOA2FKY2Tavh4nAUXunk,889
|
5
|
-
cool_seq_tool/schemas.py,sha256=miroNMyC1i6I4OuMZwJ0WQq3dBhtvuYPsMevahWQI5k,15697
|
6
|
-
cool_seq_tool/utils.py,sha256=EkDFKh6allYu_BaODuosALECm8z64JiovXC8yHd2kHY,1583
|
7
|
-
cool_seq_tool/version.py,sha256=00BKrYQ_DDUCwzibwzXpM7JCXVp-i5tZlTE4r8vs2eA,57
|
8
|
-
cool_seq_tool/data/__init__.py,sha256=EAk0f_xeq1JAkRosLMiWWhEXku6lYfMZ63HR_6QxSqs,77
|
9
|
-
cool_seq_tool/data/data_downloads.py,sha256=Jlt9YYxkJdUuDwXmuRheZ7D4deArlYLQUNsr4CQwYNE,3747
|
10
|
-
cool_seq_tool/data/transcript_mapping.tsv,sha256=AO3luYQAbFiCoRgiiPXotakb5pAwx1jDCeXpvGdIuac,24138769
|
11
|
-
cool_seq_tool/handlers/__init__.py,sha256=xDQ84N4ImrUBKwGmrg64yGUMh0ArW-DwjJuTkKrIJL4,77
|
12
|
-
cool_seq_tool/handlers/seqrepo_access.py,sha256=JVkfMnRMiNtsZOqsXZYgGT6XhtXTti6qw7MINj3Rwmc,9065
|
13
|
-
cool_seq_tool/mappers/__init__.py,sha256=5aE6IRTG8SwOofFR19QHmK-1n2PaKwEPzFGNE0_HS3s,261
|
14
|
-
cool_seq_tool/mappers/alignment.py,sha256=htGb9rJab8dAKcMR62NF0uGc5l4KROrMcMAKfSQhva0,9620
|
15
|
-
cool_seq_tool/mappers/exon_genomic_coords.py,sha256=BH3BIEUOrccjtqVxlkl-LQt5f8BXCvFmCJfVfb5qgYI,30863
|
16
|
-
cool_seq_tool/mappers/mane_transcript.py,sha256=h7J4ip9HPhVvADqvWp5ZGT9257xymVkSJ3vj3YRzIws,49359
|
17
|
-
cool_seq_tool/routers/__init__.py,sha256=x00Dq0LzqYoBPbipmyexLbAMUb7Udx8DozfwT-mJo1E,436
|
18
|
-
cool_seq_tool/routers/default.py,sha256=F9NDKv7oiEz7Yk9BKAqhJxTBELpYLDhOqB8keRVtYkU,3937
|
19
|
-
cool_seq_tool/routers/mane.py,sha256=CKXAwIQOyfEhEiRCVMqzDesbijkUIFnvxx8mKPyxDXk,3547
|
20
|
-
cool_seq_tool/routers/mappings.py,sha256=I9hxriBlkv9vQp1l_17L-VxQSUJ9-IyLyqwXGue4axg,6091
|
21
|
-
cool_seq_tool/sources/__init__.py,sha256=lERBM8cOqlJhYqz_DwOMV5FsWvMvQMbU1KQBxx_cz6M,303
|
22
|
-
cool_seq_tool/sources/mane_transcript_mappings.py,sha256=Bah16WhfBk3Def3ehYvccR13lO90f8Bib8rj8zbszVs,3753
|
23
|
-
cool_seq_tool/sources/transcript_mappings.py,sha256=Gz1PCf54RDApY5QfZqP8vm4iHCHLv-Ar4cy5Dj4cAe4,9797
|
24
|
-
cool_seq_tool/sources/uta_database.py,sha256=DYAH0oxxURyRbeRLlD3AQOi4BiTIlZbzsI05Lt6x68Y,44007
|
25
|
-
cool_seq_tool-0.4.0.dev1.dist-info/LICENSE,sha256=1jbnPcw_qmlDZyD_E_ebjWwjIvBgOD-1biodvBtSl1U,1072
|
26
|
-
cool_seq_tool-0.4.0.dev1.dist-info/METADATA,sha256=8wTeGZAxB0D2bebhpIvdp05_ehWLEnV62po7ugBCJY0,5658
|
27
|
-
cool_seq_tool-0.4.0.dev1.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
|
28
|
-
cool_seq_tool-0.4.0.dev1.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
|
29
|
-
cool_seq_tool-0.4.0.dev1.dist-info/RECORD,,
|
File without changes
|
File without changes
|
File without changes
|