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Tiledb unified ingest #9

Merged
merged 16 commits into from
Nov 18, 2024
Merged

Tiledb unified ingest #9

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badd7a6
Branch for ingestin of tiledb_unified
Oct 15, 2024
12135e0
Branch for ingestin of tiledb_unified
bruno-ariano Oct 15, 2024
b79a656
Branch for ingestin of tiledb_unified
bruno-ariano Oct 15, 2024
20d9986
adjusting for sha
bruno-ariano Oct 18, 2024
7825f56
Merge branch 'main' of github.com:ht-diva/gwasstudio into tiledb_unif…
bruno-ariano Oct 18, 2024
ccad1de
complete ingestion edits
bruno-ariano Oct 21, 2024
17994a9
modify export
bruno-ariano Oct 31, 2024
eaaa82f
modify export
bruno-ariano Oct 31, 2024
7ce73f6
modify export
bruno-ariano Oct 31, 2024
bfecf30
fix export version2
bruno-ariano Oct 31, 2024
6599bc4
adding export
bruno-ariano Nov 4, 2024
c6a58e0
adding export
bruno-ariano Nov 4, 2024
32c538a
adding polars to snp selection
bruno-ariano Nov 4, 2024
ff8fe5b
include polars dependency
gmauro Nov 18, 2024
4b96ad8
fix conflict on main
gmauro Nov 18, 2024
4e91c5e
add pandas dependency
gmauro Nov 18, 2024
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56,511 changes: 56,511 additions & 0 deletions data/ensembl_gene_annotations.txt
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0 gwasstudio/data/README.md → data/hapmap3/README.md
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0 gwasstudio/data/convert_rsid.R → data/hapmap3/convert_rsid.R
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2 changes: 1 addition & 1 deletion gwasstudio/data/hapmap3_snps.csv → data/hapmap3/hapmap3_snps.csv
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0 gwasstudio/data/hapmap3_snps_ID.csv → data/hapmap3/hapmap3_snps_ID.csv
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142 changes: 42 additions & 100 deletions gwasstudio/cli/export.py
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1 change: 0 additions & 1 deletion gwasstudio/cli/info.py
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75 changes: 44 additions & 31 deletions gwasstudio/cli/ingest.py
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0 gwasstudio/cli/__init__.py → gwasstudio/functions/__init__.py
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23 changes: 23 additions & 0 deletions gwasstudio/functions/create_tiledb_schema.py
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29 changes: 29 additions & 0 deletions gwasstudio/functions/process_and_ingest.py
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16 changes: 8 additions & 8 deletions gwasstudio/main.py
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56 changes: 0 additions & 56 deletions gwasstudio/methods/extract_snp.py
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91 changes: 26 additions & 65 deletions gwasstudio/methods/locus_breaker.py
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1 change: 1 addition & 0 deletions gwasstudio/test_snp_single_traitid_.txt
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3 changes: 3 additions & 0 deletions gwasstudio/test_snp_traitid.txt
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95 changes: 94 additions & 1 deletion gwasstudio/utils/__init__.py
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2 changes: 2 additions & 0 deletions pyproject.toml
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