78a15f21fb3bfad23eac7217e6d831810558304e
angie
  Thu Sep 2 17:50:15 2021 -0700
Adding note about COG-UK credits in BioSample text (although I should repeat with the new biosample.jsonl file).

diff --git src/hg/utils/otto/sarscov2phylo/publicCredits.sh src/hg/utils/otto/sarscov2phylo/publicCredits.sh
index e50d582..51c367f 100755
--- src/hg/utils/otto/sarscov2phylo/publicCredits.sh
+++ src/hg/utils/otto/sarscov2phylo/publicCredits.sh
@@ -1,70 +1,84 @@
 #!/bin/bash
 set -beEu -x -o pipefail
 
 #	Do not modify this script, modify the source tree copy:
 #	kent/src/hg/utils/otto/sarscov2phylo/publicCredits.sh
 
 usage() {
     echo "usage: $0"
 }
 
 if [ $# != 0 ]; then
   usage
   exit 1
 fi
 
 cncbMetadata=/hive/data/outside/otto/sarscov2phylo/cncb.latest/cncb.metadata.tsv
 ncbiMetadata=ncbi.authors.20-11-13.csv
 #*** TODO AUTOMATE ME
 #   * https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=SARS-CoV-2,%20taxid:2697049
 #   * Download button
 #   * Current table view result --> CSV format, Next button
 #   * Download all records, Next button
 #   * Select Accession and Authors [no labs options unfortunately]
 #   * Download button, save as ncbi.authors.date.csv
 
 #*** TODO AUTOMATE ME
 #   * https://www.ebi.ac.uk/ena/browser/view/PRJEB37886
 #   * select columns center_name, sample_accession, sample_alias
 #   * Download report: TSV
 #   * file saved to filereport_read_run_PRJEB37886_tsv.2020-11-3.txt (extra first column, run_accession)
 # 2021-01-08: the project seems to have 133312 sequences, but the download file is cut off
 # after 100,000.  It would probably be more efficient to just identify all of the country/center
 # strings in strain names, and ask COG-UK how to attribute sequences from each one.
 cogUkMetadata=filereport_read_run_PRJEB37886_tsv.2020-11-13.txt
 
 
+# Actually BioSample has this for COG-UK:
+# xzcat $ncbiDir/all.bioSample.tab.xz \
+# | grep COG-UK \
+# | sed -re 's@COG-UK/@@; s/(\t202[01])[0-9-]+/\1/;' \
+# | tawk '{print $8 "/" $3 "/" $4, $5;}' \
+# | sort > cogToLab
+# -- although some entries break it down like this:
+# Wales/QEUH-B2C4CB/2020  Originating lab: Wales Specialist Virology Centre Sequencing lab: Pathogen Genomics Unit
+# -- well, I guess just that one:
+# g : cogToLab | cut -f 2 | sort | uniq -c | sort -nr | less
+#  38415 Originating lab: Wales Specialist Virology Centre Sequencing lab: Pathogen Genomics Unit
+
+
+
 # Author credits file... strip GenBank version numbers because NCBI metadata doesn't have those
 cut -f 2 treeToPublic \
 | cut -d \| -f 2 \
 | sed -re 's/^([A-Z][A-Z][0-9]{6})\.[0-9]/\1/;' \
 | sort > publicIdsInTree
 tail -n+2 $cncbMetadata \
 | cut -f 2,12,14 \
 | grep -v ^EPI_ISL_ \
 | egrep -v '^[A-Z][A-Z][0-9]{6}' \
 | sed -e 's/"//g; s/$/\tn\/a/;' \
   > cncb.credits
 tail -n+2 $ncbiMetadata \
 | csvToTab \
 | tawk '{print $1, "n/a", "n/a", $2;}' \
   > ncbi.credits
 tail -n+2 $cogUkMetadata \
 | tawk '{print $4, $3, $3, "COVID-19 Genomics UK Consortium";}' \
 | sed -e 's@^COG-UK/@@;' \
 | sort -u \
   > cogUk.credits.partialIds
 grep / publicIdsInTree \
 | awk -F/ '{print $2 "\t" $0;}' \
 | sort \
   > cogUk.partialToFull
 join -a 2 -e "n/a" -t$'\t' -o 2.2,1.2,1.3,1.4 cogUk.credits.partialIds cogUk.partialToFull \
 | tawk '{ if ($4 == "n/a") { $4 = "COVID-19 Genomics UK Consortium"; } print; }' \
   > cogUk.credits
 /bin/echo -e "accession\toriginating_lab\tsubmitting_lab\tauthors" > acknowledgements.tsv
 
 #*** THIS IS just for the subset... we need a full acknowledgements file too.
 grep -Fwf publicIdsInTree cncb.credits >> acknowledgements.tsv
 grep -Fwf publicIdsInTree ncbi.credits >> acknowledgements.tsv
 grep -Fwf publicIdsInTree cogUk.credits >> acknowledgements.tsv
 gzip acknowledgements.tsv