99599c7130790107ff0de9f043930da6aa7fddf1
angie
  Mon Nov 16 16:35:58 2020 -0800
Scripts for automating SARS-CoV-2 Phylogeny tracks (refs #26530): fetching
sequences and metadata from several public sources, mapping GISAID IDs to
public seq IDs, downloading the latest release of the phylogenetic tree from
github.com/roblanf/sarscov2phylo/ , making VCFs from GISAID and public
sequences, and using github.com/yatisht/usher to resolve ambiguous alleles,
make protobuf files for hgPhyloPlace, and add public sequences that have not
been mapped to GISAID sequences to the sarscov2phylo tree for a comprehensive
public tree+VCF.

This is still not fully otto-mated because certain crucial inputs like
GISAID sequences still must be downloaded using a web browser, but the goal
is to automate as much as possible and maybe someday have it fully cron-driven.

There are two main top-level scripts which call other scripts, which may in turn
call scripts, in this hierarchy:

updateIdMapping.sh
getCogUk.sh
getNcbi.sh
searchAllSarsCov2BioSample.sh
bioSampleIdToText.sh
bioSampleTextToTab.pl
gbMetadataAddBioSample.pl
fixNcbiFastaNames.pl

updateSarsCov2Phylo.sh
getRelease.sh
processRelease.sh
cladeLineageColors.pl
mapPublic.sh
extractUnmappedPublic.sh
addUnmappedPublic.sh

many of the above:
util.sh

publicCredits.sh will hopefully be folded into updateSarsCov2Phylo.sh when I
figure out how to automate fetching of author/institution metadata from NCBI
and COG-UK.

diff --git src/hg/utils/otto/sarscov2phylo/getCogUk.sh src/hg/utils/otto/sarscov2phylo/getCogUk.sh
new file mode 100755
index 0000000..d2a2e2c
--- /dev/null
+++ src/hg/utils/otto/sarscov2phylo/getCogUk.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+set -beEu -o pipefail
+
+# Download latest COG-UK fasta and metadata; update $ottoDir/cogUk.latest link.
+
+scriptDir=$(dirname "${BASH_SOURCE[0]}")
+source $scriptDir/util.sh
+
+today=$(date +%F)
+
+ottoDir=/hive/data/outside/otto/sarscov2phylo
+cogUrlBase=https://cog-uk.s3.climb.ac.uk/phylogenetics/latest
+
+mkdir -p $ottoDir/cogUk.$today
+cd $ottoDir/cogUk.$today
+
+wget -q $cogUrlBase/cog_all.fasta
+wget -q $cogUrlBase/cog_metadata.csv
+
+xz -f -T 50 cog_all.fasta
+
+tail -n +2 cog_metadata.csv \
+| awk -F, '{print $1 "\t" $4;}' | sort > cogUkToDate
+
+rm -f $ottoDir/cogUk.latest
+ln -s cogUk.$today $ottoDir/cogUk.latest