cool-seq-tool 0.4.0.dev2__py3-none-any.whl → 0.4.1__py3-none-any.whl

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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 @@
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- """Provide paths to shared files, and trigger data acquisition if unavailable."""
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- from os import environ
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- from pathlib import Path
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-
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- from cool_seq_tool.data.data_downloads import DataDownload
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-
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- APP_ROOT = Path(__file__).resolve().parents[0]
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-
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- TRANSCRIPT_MAPPINGS_PATH = Path(
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- environ.get("TRANSCRIPT_MAPPINGS_PATH", f"{APP_ROOT}/data/transcript_mapping.tsv")
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- )
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-
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- d = DataDownload()
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-
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- provided_mane_summary_path = environ.get("MANE_SUMMARY_PATH", "")
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- if provided_mane_summary_path:
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- MANE_SUMMARY_PATH = Path(provided_mane_summary_path)
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- else:
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- MANE_SUMMARY_PATH = d.get_mane_summary()
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-
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- provided_lrg_refseq_path = environ.get("LRG_REFSEQGENE_PATH", "")
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- if provided_lrg_refseq_path:
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- LRG_REFSEQGENE_PATH = Path(provided_lrg_refseq_path)
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- else:
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- LRG_REFSEQGENE_PATH = d.get_lrg_refseq_gene_data()
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-
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-
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- 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 @@
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- cool_seq_tool/__init__.py,sha256=eBycAZIAJBCf51xQLQYHzvUep1i21LMrzBdRLqfe-Fc,352
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- cool_seq_tool/api.py,sha256=3Pc0j0pHMZ_3skTkjDlQpcu_MM6kyNPmBrwm_LrH-rw,1234
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- cool_seq_tool/app.py,sha256=3r2hlajW6xjf3u_Uf9WlqMfBEK-LnB74sG2UpJlj2bY,3757
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- cool_seq_tool/paths.py,sha256=7EA21Vmf9hvct0z_V4oK0WTWOA2FKY2Tavh4nAUXunk,889
5
- cool_seq_tool/schemas.py,sha256=Uw5OkC0dPM_RC8ZHNn1wLZBZK_kWAkkQQRrh-zOsJjg,15922
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- cool_seq_tool/utils.py,sha256=26y_25V029l-ra3We3z-KQFfgRlcvfl2dQ8XJ1t6yfM,1625
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- cool_seq_tool/version.py,sha256=cuIT6sKXUqxwO7uw5ifUO0f7jv19ApxBFZMLy2jwNgo,57
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- cool_seq_tool/data/__init__.py,sha256=pOdws59_iPOP0V4xqx55PdxCUxHSA5N_Eo5L0oZsafs,63
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- cool_seq_tool/data/data_downloads.py,sha256=WaTxeCnifBuif89_lo6hFrmTu2gu8Jy8ndB9crcqvFQ,3869
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- cool_seq_tool/data/transcript_mapping.tsv,sha256=AO3luYQAbFiCoRgiiPXotakb5pAwx1jDCeXpvGdIuac,24138769
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- cool_seq_tool/handlers/__init__.py,sha256=xDQ84N4ImrUBKwGmrg64yGUMh0ArW-DwjJuTkKrIJL4,77
12
- cool_seq_tool/handlers/seqrepo_access.py,sha256=XUS4zjguXB7OfLZLnQatWwiYVspu87rk50v1WzENvXE,9029
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- cool_seq_tool/mappers/__init__.py,sha256=5aE6IRTG8SwOofFR19QHmK-1n2PaKwEPzFGNE0_HS3s,261
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- cool_seq_tool/mappers/alignment.py,sha256=htGb9rJab8dAKcMR62NF0uGc5l4KROrMcMAKfSQhva0,9620
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- cool_seq_tool/mappers/exon_genomic_coords.py,sha256=vuU1vtEzgwGqGFywDOEia8I-46qsAhRI1fM_PkbpBnk,30809
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- cool_seq_tool/mappers/mane_transcript.py,sha256=XB51pcR5TCtteXS525NgP2S7aRU1gnBtB2ZrSltxM1A,49364
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- cool_seq_tool/routers/__init__.py,sha256=x00Dq0LzqYoBPbipmyexLbAMUb7Udx8DozfwT-mJo1E,436
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- cool_seq_tool/routers/default.py,sha256=nMDcAAdo-QZugs6k43HnYJCzhorg9nFt0TsdXTckVZU,3927
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- cool_seq_tool/routers/mane.py,sha256=fASm7wo4ZjYB5l8G5cu4zqObwf811SxLVCJhbeqC_cY,3544
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- cool_seq_tool/routers/mappings.py,sha256=I9hxriBlkv9vQp1l_17L-VxQSUJ9-IyLyqwXGue4axg,6091
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- cool_seq_tool/sources/__init__.py,sha256=lERBM8cOqlJhYqz_DwOMV5FsWvMvQMbU1KQBxx_cz6M,303
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- cool_seq_tool/sources/mane_transcript_mappings.py,sha256=Oyq7cdUJ2j0isROCkHW-rgtU7LtyFon3DJz6hrEl5cU,3750
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- cool_seq_tool/sources/transcript_mappings.py,sha256=_CV71tyge24rr7Kb_rJJQTr9uG1lSU_O-HcC9hIc5OQ,9731
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- cool_seq_tool/sources/uta_database.py,sha256=nlvEIsdZxY7z4-PfTWVbpt5O4fMNgHWHmFxx3lL-mgM,43578
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- 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
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- 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
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- cool_seq_tool-0.4.0.dev2.dist-info/RECORD,,