cool-seq-tool 0.4.0.dev2__py3-none-any.whl → 0.4.1__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.
Files changed (33) hide show
  1. cool_seq_tool/__init__.py +1 -3
  2. cool_seq_tool/api.py +1 -2
  3. cool_seq_tool/app.py +42 -24
  4. cool_seq_tool/handlers/__init__.py +1 -0
  5. cool_seq_tool/handlers/seqrepo_access.py +13 -15
  6. cool_seq_tool/mappers/__init__.py +1 -0
  7. cool_seq_tool/mappers/alignment.py +5 -6
  8. cool_seq_tool/mappers/exon_genomic_coords.py +232 -68
  9. cool_seq_tool/mappers/mane_transcript.py +84 -86
  10. cool_seq_tool/resources/__init__.py +1 -0
  11. cool_seq_tool/resources/data_files.py +93 -0
  12. cool_seq_tool/resources/status.py +151 -0
  13. cool_seq_tool/routers/__init__.py +1 -0
  14. cool_seq_tool/routers/default.py +1 -0
  15. cool_seq_tool/routers/mane.py +4 -4
  16. cool_seq_tool/routers/mappings.py +2 -2
  17. cool_seq_tool/schemas.py +83 -37
  18. cool_seq_tool/sources/__init__.py +1 -0
  19. cool_seq_tool/sources/mane_transcript_mappings.py +14 -7
  20. cool_seq_tool/sources/transcript_mappings.py +41 -32
  21. cool_seq_tool/sources/uta_database.py +120 -69
  22. cool_seq_tool/utils.py +2 -2
  23. cool_seq_tool/version.py +2 -1
  24. {cool_seq_tool-0.4.0.dev2.dist-info → cool_seq_tool-0.4.1.dist-info}/LICENSE +1 -1
  25. {cool_seq_tool-0.4.0.dev2.dist-info → cool_seq_tool-0.4.1.dist-info}/METADATA +15 -8
  26. cool_seq_tool-0.4.1.dist-info/RECORD +29 -0
  27. {cool_seq_tool-0.4.0.dev2.dist-info → cool_seq_tool-0.4.1.dist-info}/WHEEL +1 -1
  28. cool_seq_tool/data/__init__.py +0 -2
  29. cool_seq_tool/data/data_downloads.py +0 -89
  30. cool_seq_tool/paths.py +0 -28
  31. cool_seq_tool-0.4.0.dev2.dist-info/RECORD +0 -29
  32. /cool_seq_tool/{data → resources}/transcript_mapping.tsv +0 -0
  33. {cool_seq_tool-0.4.0.dev2.dist-info → cool_seq_tool-0.4.1.dist-info}/top_level.txt +0 -0
cool_seq_tool/paths.py DELETED
@@ -1,28 +0,0 @@
1
- """Provide paths to shared files, and trigger data acquisition if unavailable."""
2
- from os import environ
3
- from pathlib import Path
4
-
5
- from cool_seq_tool.data.data_downloads import DataDownload
6
-
7
- APP_ROOT = Path(__file__).resolve().parents[0]
8
-
9
- TRANSCRIPT_MAPPINGS_PATH = Path(
10
- environ.get("TRANSCRIPT_MAPPINGS_PATH", f"{APP_ROOT}/data/transcript_mapping.tsv")
11
- )
12
-
13
- d = DataDownload()
14
-
15
- provided_mane_summary_path = environ.get("MANE_SUMMARY_PATH", "")
16
- if provided_mane_summary_path:
17
- MANE_SUMMARY_PATH = Path(provided_mane_summary_path)
18
- else:
19
- MANE_SUMMARY_PATH = d.get_mane_summary()
20
-
21
- provided_lrg_refseq_path = environ.get("LRG_REFSEQGENE_PATH", "")
22
- if provided_lrg_refseq_path:
23
- LRG_REFSEQGENE_PATH = Path(provided_lrg_refseq_path)
24
- else:
25
- LRG_REFSEQGENE_PATH = d.get_lrg_refseq_gene_data()
26
-
27
-
28
- SEQREPO_ROOT_DIR = environ.get("SEQREPO_ROOT_DIR", "/usr/local/share/seqrepo/latest")
cool_seq_tool-0.4.0.dev2.dist-info/RECORD DELETED
@@ -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=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,,