From 6d6c230e4d8d1efbca8d6a5abf838dd99b846b3d Mon Sep 17 00:00:00 2001 From: jfy133 Date: Sat, 30 Sep 2023 09:13:19 +0000 Subject: [PATCH 1/3] [skip ci] Update AncientMetagenomeDir geojson --- .../figures/ancientmetagenomedir.geojson | 5073 +++++++++-------- 1 file changed, 2538 insertions(+), 2535 deletions(-) diff --git a/assets/images/figures/ancientmetagenomedir.geojson b/assets/images/figures/ancientmetagenomedir.geojson index 4a630c3c3..41143f0e2 100644 --- a/assets/images/figures/ancientmetagenomedir.geojson +++ b/assets/images/figures/ancientmetagenomedir.geojson @@ -1,1397 +1,1397 @@ { "type": "FeatureCollection", "features": [ -{ "type": "Feature", "properties": { "project_name": "Ahmed2018", "publication_year": 2018, "publication_doi": "10.1016/j.quascirev.2017.11.037", "site_name": "Hässeldala Port", "latitude": 56.16, "longitude": 15.01, "geo_loc_name": "Sweden", "study_primary_focus": "microbial", "sequence_name": "Sediment core #7.4", "depth": 435.0, "sample_name": "HA1.1", "sample_age": 13900, "sample_age_doi": "10.3389/fevo.2019.00189", "feature": "lake", "material": "lake sediment", "sampling_date": 2015.0, "archive": "ENA", "archive_project": "PRJNA378719", "archive_accession": "SRS2040659", "dir_type": "Ancient Metagenome - 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ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/091/ERR10822091/ERR10822091.fastq.gz 4d93d79f34612c23da1d931fc31871ca 4278163 Clavel2023 2023 10.1016/j.isci.2023.106787 MAJ38 ENA PRJEB59234 ERS14555592 MAJ38t6_Ages_2_8153_lr03_i03_SN1 double AccuPrime Pfx DNA half-udg Illumina MiniSeq PAIRED Targeted-Capture 18911 ERR10822438 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/038/ERR10822438/ERR10822438_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/038/ERR10822438/ERR10822438_2.fastq.gz 755eb7c0958a7286895a07358211d721;94b8a89f869e88c85e290addaa99ccef 906081;944788 Clavel2023 2023 10.1016/j.isci.2023.106787 MAJ38 ENA PRJEB59234 ERS14555592 MAJ38t6_Ages_2_8153_lr16_i26_SN2 double AccuPrime Pfx DNA half-udg Illumina MiniSeq PAIRED Targeted-Capture 69510 ERR10822439 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR10822439/MAJ38_E6_L18_R1_M.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR10822439/MAJ38_E6_L18_R2_M.fastq.gz 5b21c69e610f47178058addd5c49674b;a559f05ff8beb017a8efaf7a1a3d7203 2939990;2939990 diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv index 4a8038837..6e900c43f 100644 --- a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv +++ b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv @@ -587,7 +587,7 @@ Swali2023 2023 10.1038/s41467-023-38393-w Charterhouse Warren, Mendip Hills, Som Swali2023 2023 10.1038/s41467-023-38393-w Levens Deer Park ring cairn, Leven, Cumbria 54.268 -2.761 United Kingdom C10928 Homo sapiens 3900 10.1038/s41467-023-38393-w bacteria Yersinia pestis tooth chromosome ENA raw PRJEB61230 ERS14909714,ERS14891343 Clavel2023 2023 10.1016/j.isci.2023.106787 La Major Cathedral, Marseille, Bouches-du-Rhône 43.3 5.365 France MAJ75 Homo sapiens 300 10.1016/j.isci.2023.106787 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB59233 ERS14555610,ERS14555611,ERS14555612,ERS14555613,ERS14555614,ERS14555615,ERS14555616,ERS14555617 Clavel2023 2023 10.1016/j.isci.2023.106787 La Major Cathedral, Marseille, Bouches-du-Rhône 43.3 5.365 France MAJ46 Homo sapiens 300 10.1016/j.isci.2023.106787 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB59233 ERS14555595,ERS14555596,ERS14555597,ERS14555598,ERS14555599,ERS14555600,ERS14555601,ERS14555602,ERS14555603,ERS14555604 -Clavel2023 2023 10.1016/j.isci.2023.106787 La Major Cathedral, Marseille, Bouches-du-Rhône 43.3 5.365 France MAJ38 Homo sapiens 300 10.1016/j.isci.2023.106787 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB59233 ERS14555592,ERS14555591,ERS14555590,ERS14555589,ERS14555588,ERS14555587 +Clavel2023 2023 10.1016/j.isci.2023.106787 La Major Cathedral, Marseille, Bouches-du-Rhône 43.3 5.365 France MAJ38 Homo sapiens 300 10.1016/j.isci.2023.106787 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB59233,PRJEB59234 ERS14555592,ERS14555591,ERS14555590,ERS14555589,ERS14555588,ERS14555587 Clavel2023 2023 10.1016/j.isci.2023.106787 Hôtel-Dieu Saint-Jean-Baptiste, Amiens 49.898 2.299 France AMIENS268 Homo sapiens 400 10.1016/j.isci.2023.106787 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB59233 ERS14555669,ERS14555670,ERS14555671 Clavel2023 2023 10.1016/j.isci.2023.106787 Les Rayettes, Martigues 43.415 5.039 France RAY1015 Homo sapiens 300 10.1016/j.isci.2023.106787 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB59233 ERS14555624,ERS14555625,ERS14555626 Clavel2023 2023 10.1016/j.isci.2023.106787 Les Rayettes, Martigues 43.415 5.039 France RAY1028 Homo sapiens 300 10.1016/j.isci.2023.106787 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB59233 ERS14555627,ERS14555628 diff --git a/assets/analysis/prerelease-validation-crosstable.R b/assets/analysis/prerelease-validation-crosstable.R index 4a4f37a1b..c1f917ead 100644 --- a/assets/analysis/prerelease-validation-crosstable.R +++ b/assets/analysis/prerelease-validation-crosstable.R @@ -33,4 +33,5 @@ cat("\n") cat("POSSIBLE PROBLEMS FOR:", paste0(unique(publication_doi_na$project_name), sep = ","), "\n") cat("EXCEPTIONS ALLOWED:\n") cat("-(ancientmetagenome-hostassociated): Klapper2023 [reseq. of FellowsYates2023 - no new samples]\n") +cat("-(ancientsinglegenome-hostassociated): Clavel2023 [Reseq of previous human study not in AMDir, different PRJ code]") cat("\n") From 228a5af2c73ba2b223d9c9471788c375423fbe4e Mon Sep 17 00:00:00 2001 From: jfy133 Date: Sat, 30 Sep 2023 09:35:30 +0000 Subject: [PATCH 3/3] [skip ci] Update AncientMetagenomeDir geojson --- .../figures/ancientmetagenomedir.geojson | 5076 ++++++++--------- 1 file changed, 2538 insertions(+), 2538 deletions(-) diff --git a/assets/images/figures/ancientmetagenomedir.geojson b/assets/images/figures/ancientmetagenomedir.geojson index 41143f0e2..98ca780f8 100644 --- a/assets/images/figures/ancientmetagenomedir.geojson +++ 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