Commits for angie
switch to files view, user index
v407_base to v408_preview (2020-11-16 to 2020-11-23) v408
Show details
9d643ff9f562c900533aac2a8dec11ebf8c90fcf Mon Nov 16 08:53:51 2020 -0800
- Add support for lineage D. refs #26530
- src/hg/makeDb/doc/wuhCor1/cladeLineageColors.pl - lines changed 7, context: html, text, full: html, text
99599c7130790107ff0de9f043930da6aa7fddf1 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.
- src/hg/utils/otto/sarscov2phylo/addUnmappedPublic.sh - lines changed 83, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/bioSampleIdToText.sh - lines changed 45, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/bioSampleTextToTab.pl - lines changed 129, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/cladeLineageColors.pl - lines changed 179, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/extractUnmappedPublic.sh - lines changed 95, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/fixNcbiFastaNames.pl - lines changed 119, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl - lines changed 97, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/getCogUk.sh - lines changed 27, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/getNcbi.sh - lines changed 83, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/getRelease.sh - lines changed 80, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/mapPublic.sh - lines changed 94, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/processRelease.sh - lines changed 123, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/publicCredits.sh - lines changed 67, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/searchAllSarsCov2BioSample.sh - lines changed 19, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh - lines changed 66, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/updateSarsCov2Phylo.sh - lines changed 40, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/util.sh - lines changed 62, context: html, text, full: html, text
7a8c6715c6b044e8e04ef55b2c9e4575112147f9 Mon Nov 16 16:46:01 2020 -0800
- Adding note that updates of sarsCov2Phylo and sarsCov2PhyloPub tracks are now done by scripts in hg/utils/otto/sarscov2phylo/ instead of copy-pasting from doc. refs #26530
- src/hg/makeDb/doc/wuhCor1/phylogenetics.txt - lines changed 8, context: html, text, full: html, text
8d5880a93fa01e34601d87638c775f5945f9b269 Tue Nov 17 15:32:54 2020 -0800
- Adding clarifications to usage message & code based on code review feedback, thanks Chris. refs #26546
- src/utils/vcfFilter/vcfFilter.c - lines changed 6, context: html, text, full: html, text
7ffce0e9718d585fa11cddf6ae4fa2be764e6795 Fri Jul 24 17:19:51 2020 -0700
- Added phyloCountInternalNodes. Allow Newick format tree node names to begin with '_'. refs #25943
3bdd753973190ec7e64d85a90ab912b9a7c37489 Fri Sep 4 13:45:27 2020 -0700
- Move leftLabelWidth parameters out of hgTracks global variables into trackLayout lib (for use by hgPhyloPlace). refs #25943
- src/hg/hgTracks/config.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.h - lines changed 3, context: html, text, full: html, text
- src/hg/hgTracks/simpleTracks.c - lines changed 15, context: html, text, full: html, text
- src/hg/inc/trackLayout.h - lines changed 5, context: html, text, full: html, text
- src/hg/lib/trackLayout.c - lines changed 12, context: html, text, full: html, text
ff6abb3b7f34ac95c918dd1f03a9e5d52c59fc20 Thu Nov 19 12:58:52 2020 -0800
- Very incomplete parser for Google's protobuf3 -- sufficient to read file generated by Yatish Turakhia's usher --save-mutation-annotated-tree. refs #25943
- src/hg/lib/protobuf.c - lines changed 286, context: html, text, full: html, text
e14c2761ca01d8175578df87bd5311b5c0442bfb Thu Nov 19 13:04:01 2020 -0800
- New CGI hgPhyloPlace: place SARS-CoV-2 genomes in fasta or VCF on phylogenetic tree using Yatish Turakhia's UShER program; add subtree custom tracks and Nextstrain linkouts to visualize results. refs #25943
- src/hg/hgPhyloPlace/hgPhyloPlace.c - lines changed 408, context: html, text, full: html, text
- src/hg/hgPhyloPlace/makefile - lines changed 29, context: html, text, full: html, text
- src/hg/hgPhyloPlace/parsimonyProto.c - lines changed 275, context: html, text, full: html, text
- src/hg/hgPhyloPlace/parsimonyProto.h - lines changed 42, context: html, text, full: html, text
- src/hg/hgPhyloPlace/phyloPlace.c - lines changed 1439, context: html, text, full: html, text
- src/hg/hgPhyloPlace/phyloPlace.h - lines changed 141, context: html, text, full: html, text
- src/hg/hgPhyloPlace/phyloPlaceMain.c - lines changed 40, context: html, text, full: html, text
- src/hg/hgPhyloPlace/runUsher.c - lines changed 767, context: html, text, full: html, text
- src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 555, context: html, text, full: html, text
- src/hg/hgPhyloPlace/vcfFromFasta.c - lines changed 519, context: html, text, full: html, text
- src/hg/hgPhyloPlace/writeCustomTracks.c - lines changed 568, context: html, text, full: html, text
switch to files view, user index