TASK-5387 - Add Polygenic Scores (PGS) #697

jtarraga · 2024-07-01T06:39:14Z

Add Polygenic Scores (PGS)

…5387

… #TASK-5407, #TASK-5387

…407, #TASK-5387

…K-5407, #TASK-5387

…ASK-5407, #TASK-5387

…-5564

…ASK-5564

…r issues, #TASK-5775, #TASK-5564

…es and taking into account the version from config file, and fix sonnar issues, #TASK-5775, #TASK-5564

…dding log messages, removing hardcode filenames, sonnar issues,..., #TASK-5775, #TASK-5564

… adding log messages, removing hardcode filenames, sonnar issues,..., #TASK-5775, #TASK-5564

… file, adding log messages, removing hardcode filenames, sonnar issues,..., #TASK-5775, #TASK-5564

…to take into account the version for miRBase and miRTarBase, #TASK-5775, #TASK-5564

…nd HGMD; and fix some sonnar issues, #TASK-5775, #TASK-5564

…-5564

… files, and rename some constants, #TASK-5776, #TASK-5564

…atest changes, #TASK-6142, #TASK-5564

…SK-6426, #TASK-5564

…ariantAnnotationCalculator file size, #TASK-6426, #TASK-5564

… #TASK-6426, #TASK-5564

…ndard values, e.g. <deletion> to <DEL>, #TASK-5576, #TASK-5564

…d by a given species, and update download options, #TASK-5575, #TASK-5564

….., #TASK-6142, #TASK-5564

…moving study info, #TASK-5576, #TASK-5564

…d update ontology downloader to take it into account, #TASK-5575, #TASK-5564

…upport, #TASK-5575, #TASK-5564

…ort, #TASK-5576, #TASK-5564

…latest changes, #TASK-6142, #TASK-5564

…142, #TASK-5564

…les; improve summary log and update downloader managers according to these changes, #TASK-5575, #TASK-5564

jtarraga and others added 30 commits December 18, 2023 14:38

lib: download polygenic scores (PGS), #TASK-5406, #TASK-5387

278fdbd

lib: update the build command to support PGS data, #TASK-5407, #TASK-…

d327c47

…5387

lib: copy PGS version file from download to generated json directory,…

fd6ac92

… #TASK-5407, #TASK-5387

lib: update the load command to support PGS data, #TASK-5410, #TASK-5387

53aa886

lib: update PGS builder according to PGS data models changes, #TASK-5…

345cd1c

…407, #TASK-5387

lib: update PGS builder according to Pubmed data models changes, #TAS…

4f44661

…K-5407, #TASK-5387

lib: add PGS manager and adaptor, #TASK-5411, #TASK-5387

436f534

lib: add support for annotating using PGS, #TASK-5411, #TASK-5387

314786d

lib: add PGS data for variant annotation, #TASK-5411, #TASK-5387

b0aeca4

lib: add MongoDB indexes for PGS collections, #TASK-5410, #TASK-5387

c6c628b

download: gwas catalog fixes

6346c97

lib: take into account the NumberFormatException, #TASK-5407, #TASK-5387

d343315

lib: improve PGS builder, #TASK-5407, #TASK-5387

268f591

lib: remove System.out in PGS builder, #TASK-5407, #TASK-5387

5972c15

lib: filter contigs (only chromosomes) when processing PGS scores, #T…

d9ad898

…ASK-5407, #TASK-5387

lib: minor changes, #TASK-5407, #TASK-5387

d3ad8c9

Merge branch 'TASK-5392' into TASK-5564

19368e6

Update configuration.yml

89264c2

core: update pubmed URLs in the configuration file, #TASK-5775, #TASK…

2be5f21

…-5564

core: update pubmed version in the configuration file, #TASK-5775, #T…

fe05795

…ASK-5564

core: improve Ontology downloader, #TASK-5775, #TASK-5564

50f7008

lib: take into account PubMed version from config file, and fix sonna…

a8a9328

…r issues, #TASK-5775, #TASK-5564

lib: improve clinvar and gwas downloader by removing hardcode filenam…

f84734e

…es and taking into account the version from config file, and fix sonnar issues, #TASK-5775, #TASK-5564

core: update clinvar version in config file, #TASK-5775, #TASK-5564

1a5ba4a

lib: improve gene downloader by updating versions from config file, a…

4cdd046

…dding log messages, removing hardcode filenames, sonnar issues,..., #TASK-5775, #TASK-5564

lib: improve repeat downloader by updating versions from config file,…

3cea3f3

… adding log messages, removing hardcode filenames, sonnar issues,..., #TASK-5775, #TASK-5564

lib: improve conservation downloader by updating versions from config…

f308f25

… file, adding log messages, removing hardcode filenames, sonnar issues,..., #TASK-5775, #TASK-5564

lib: update regulation download manager, and the configuration file, …

2e6e895

…to take into account the version for miRBase and miRTarBase, #TASK-5775, #TASK-5564

lib: update configuration file; and create version files for COSMIC a…

a6688d0

…nd HGMD; and fix some sonnar issues, #TASK-5775, #TASK-5564

lib: update CellBase builder for clinical variants, #TASK-5776, #TASK…

c2345d4

…-5564

jtarraga added 30 commits August 1, 2024 19:00

lib: add VariantBuilder to generate the variation JSON files from VCF…

d693f57

… files, and rename some constants, #TASK-5776, #TASK-5564

app: update the CellBase loader for variation data according to the l…

38400c1

…atest changes, #TASK-6142, #TASK-5564

app: add check before building variation data, #TASK-5776, #TASK-5564

3117337

lib: skip API-KEY param when parsing variant quey, #TASK-5564

9c810e7

server: update RESTful server to take into account multi-species, #TA…

ec5f21a

…SK-6426, #TASK-5564

lib: extract the FutureSpliceScoreAnnotator in a file to reduce the V…

36c3609

…ariantAnnotationCalculator file size, #TASK-6426, #TASK-5564

lib: update the VariantAnnotationCalculator to support multi-species,…

efa4824

… #TASK-6426, #TASK-5564

lib: add log messages in protein builder, #TASK-5776, #TASK-5564

4326fa3

lib: set variant ID in VariantBuilder, #TASK-5576, #TASK-5564

2c7ddfb

lib: remove System.exit, #TASK-5576, #TASK-5564

78211d0

lib: fix VariationBuilder by converting SV values from Ensembl to sta…

e0c6a13

…ndard values, e.g. <deletion> to <DEL>, #TASK-5576, #TASK-5564

lib: add new command 'data-list' to display the list of data supporte…

81e4cb1

…d by a given species, and update download options, #TASK-5575, #TASK-5564

app: update build options and fix sonnar issues, #TASK-5576, #TASK-5564

280fd67

app: update CLI option descriptions for loading, exporting, indexing.…

2235e5c

….., #TASK-6142, #TASK-5564

test: update JUnit tests according to the latest changes, #TASK-5564

6a4c16a

lib: improve variation builder by setting xref and annotation, and re…

68c9f43

…moving study info, #TASK-5576, #TASK-5564

lib: remove break for testing, #TASK-5576, #TASK-5564

914b9c1

core: add ontology data into configuration file for "mus musculus" an…

3538e14

…d update ontology downloader to take it into account, #TASK-5575, #TASK-5564

lib: update ontology downloader and take into account multi-species s…

d0d92a3

…upport, #TASK-5575, #TASK-5564

lib: update ontology builder and take into account multi-species supp…

d51114b

…ort, #TASK-5576, #TASK-5564

app: update load command executor for ontology data according to the …

24450d3

…latest changes, #TASK-6142, #TASK-5564

app: check data according to the species before loading data, #TASK-6…

132382d

…142, #TASK-5564

app: fix sonnar issues, #TASK-6142, #TASK-5564

d556c4c

lib: fix the function to save status and message of the downloaded fi…

1f3572c

…les; improve summary log and update downloader managers according to these changes, #TASK-5575, #TASK-5564

Merge branch 'develop' into TASK-5564

6056655

core: add dbSNP in config file (removed after merging), #TASK-5564

a8d6368

Merge branch 'TASK-5564' into TASK-5387

2950c0e

lib: limit WriteBatch for number of items, #TASK-5407, #TASK-5387

2889192

lib: improve PGS builder, #TASK-5407, #TASK-5387

8c8a4ea

lib: fix sonnar issues, #TASK-5407, #TASK-5387

28a57ba

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TASK-5387 - Add Polygenic Scores (PGS) #697

TASK-5387 - Add Polygenic Scores (PGS) #697

jtarraga commented Jul 1, 2024

TASK-5387 - Add Polygenic Scores (PGS) #697

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TASK-5387 - Add Polygenic Scores (PGS) #697

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jtarraga commented Jul 1, 2024