Skip to content

Commit

Permalink
Add rules for merging USVI data with NCBI GenBank ingested data.
Browse files Browse the repository at this point in the history 
The original Zika build contained USVI data that had been posted publiclly to
GitHub but not yet submitted to NCBI GenBank. This commit adds rules to merge
the USVI data with the NCBI GenBank data.

Since USVI does not have a genbank_accession column, we create a new accession column
for both USVI and NCBI GenBank accessions. This accession column is then used
as the strain_id column for the phylogenetic build.

Since auspice automagically generates a NCBI GenBank url for "genbank_accession" fields,
we use a "url" field instead, allowing for a mix of GenBank and GitHub urls
to be used in the strain popup window.
  • Loading branch information
@j23414
j23414 committed Nov 21, 2023
1 parent a53b5e4 commit 870c938
Show file tree
Hide file tree
Showing 7 changed files with 235 additions and 43 deletions.
14 changes: 8 additions & 6 deletions phylogenetic/Snakefile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@ rule files:

files = rules.files.params

include: "workflow/snakemake_rules/usvi.smk"

rule download:
"""Downloading sequences and metadata from data.nextstrain.org"""
output:
Expand Down Expand Up @@ -53,8 +55,8 @@ rule filter:
- minimum genome length of {params.min_length} (50% of Zika virus genome)
"""
input:
sequences = "data/sequences.fasta",
metadata = "data/metadata.tsv",
sequences = "data/sequences_all.fasta",
metadata = "data/metadata_all.tsv",
exclude = files.dropped_strains
output:
sequences = "results/filtered.fasta"
Expand Down Expand Up @@ -122,7 +124,7 @@ rule refine:
input:
tree = "results/tree_raw.nwk",
alignment = "results/aligned.fasta",
metadata = "data/metadata.tsv"
metadata = "data/metadata_all.tsv"
output:
tree = "results/tree.nwk",
node_data = "results/branch_lengths.json"
Expand Down Expand Up @@ -189,7 +191,7 @@ rule traits:
"""
input:
tree = "results/tree.nwk",
metadata = "data/metadata.tsv"
metadata = "data/metadata_all.tsv"
output:
node_data = "results/traits.json",
params:
Expand All @@ -212,7 +214,7 @@ rule export:
"""Exporting data files for for auspice"""
input:
tree = "results/tree.nwk",
metadata = "data/metadata.tsv",
metadata = "data/metadata_all.tsv",
branch_lengths = "results/branch_lengths.json",
traits = "results/traits.json",
nt_muts = "results/nt_muts.json",
Expand Down Expand Up @@ -242,7 +244,7 @@ rule export:
rule final_strain_name:
input:
auspice_json="results/raw_zika.json",
metadata="data/metadata.tsv",
metadata="data/metadata_all.tsv",
root_sequence="results/raw_zika_root-sequence.json",
output:
auspice_json="auspice/zika.json",
Expand Down
2 changes: 1 addition & 1 deletion phylogenetic/config/config_zika.yaml
View file
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
strain_id_field: "genbank_accession"
strain_id_field: "accession"
display_strain_field: "strain"
70 changes: 35 additions & 35 deletions phylogenetic/example_data/metadata.tsv
View file
Original file line number Diff line number Diff line change
@@ -1,35 +1,35 @@
strain virus genbank_accession date region country division city db segment authors url
PAN/CDC_259359_V1_V3/2015 zika KX156774 2015-12-18 North America Panama Panama Panama genbank genome Shabman et al https://www.ncbi.nlm.nih.gov/nuccore/KX156774
COL/FLR_00024/2015 zika MF574569 2015-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al https://www.ncbi.nlm.nih.gov/nuccore/MF574569
PRVABC59 zika KU501215 2015-12-XX North America Puerto Rico Puerto Rico Puerto Rico genbank genome Lanciotti et al https://www.ncbi.nlm.nih.gov/nuccore/KU501215
COL/FLR_00008/2015 zika MF574562 2015-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al https://www.ncbi.nlm.nih.gov/nuccore/MF574562
Colombia/2016/ZC204Se zika KY317939 2016-01-06 South America Colombia Colombia Colombia genbank genome Quick et al https://www.ncbi.nlm.nih.gov/nuccore/KY317939
ZKC2/2016 zika KX253996 2016-02-16 Oceania American Samoa American Samoa American Samoa genbank genome Wu et al https://www.ncbi.nlm.nih.gov/nuccore/KX253996
VEN/UF_1/2016 zika KX702400 2016-03-25 South America Venezuela Venezuela Venezuela genbank genome Blohm et al https://www.ncbi.nlm.nih.gov/nuccore/KX702400
DOM/2016/BB_0059 zika KY785425 2016-04-04 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785425
BRA/2016/FC_6706 zika KY785433 2016-04-08 South America Brazil Brazil Brazil genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785433
DOM/2016/BB_0183 zika KY785420 2016-04-18 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785420
EcEs062_16 zika KX879603 2016-04-XX South America Ecuador Ecuador Ecuador genbank genome Marquez et al https://www.ncbi.nlm.nih.gov/nuccore/KX879603
HND/2016/HU_ME59 zika KY785418 2016-05-13 North America Honduras Honduras Honduras genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785418
DOM/2016/MA_WGS16_011 zika KY785484 2016-06-06 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785484
DOM/2016/BB_0433 zika KY785441 2016-06-13 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785441
USA/2016/FL022 zika KY075935 2016-07-22 North America Usa Usa Usa genbank genome Grubaugh et al https://www.ncbi.nlm.nih.gov/nuccore/KY075935
SG_027 zika KY241697 2016-08-27 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al https://www.ncbi.nlm.nih.gov/nuccore/KY241697
SG_074 zika KY241744 2016-08-28 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al https://www.ncbi.nlm.nih.gov/nuccore/KY241744
SG_056 zika KY241726 2016-08-28 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al https://www.ncbi.nlm.nih.gov/nuccore/KY241726
USA/2016/FLUR022 zika KY325473 2016-08-31 North America Usa Usa Usa genbank genome Grubaugh et al https://www.ncbi.nlm.nih.gov/nuccore/KY325473
Aedes_aegypti/USA/2016/FL05 zika KY075937 2016-09-09 North America Usa Usa Usa genbank genome Grubaugh et al https://www.ncbi.nlm.nih.gov/nuccore/KY075937
SG_018 zika KY241688 2016-09-13 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al https://www.ncbi.nlm.nih.gov/nuccore/KY241688
USA/2016/FLWB042 zika KY325478 2016-09-26 North America Usa Usa Usa genbank genome Grubaugh et al https://www.ncbi.nlm.nih.gov/nuccore/KY325478
COL/PRV_00028/2015 zika MF574578 2016-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al https://www.ncbi.nlm.nih.gov/nuccore/MF574578
Thailand/1610acTw zika MF692778 2016-10-XX Southeast Asia Thailand Thailand Thailand genbank genome Lin et al https://www.ncbi.nlm.nih.gov/nuccore/MF692778
1_0087_PF zika KX447509 2013-12-XX Oceania French Polynesia French Polynesia French Polynesia genbank genome Pettersson et al https://www.ncbi.nlm.nih.gov/nuccore/KX447509
1_0199_PF zika KX447519 2013-11-XX Oceania French Polynesia French Polynesia French Polynesia genbank genome Pettersson et al https://www.ncbi.nlm.nih.gov/nuccore/KX447519
1_0181_PF zika KX447512 2013-12-XX Oceania French Polynesia French Polynesia French Polynesia genbank genome Pettersson et al https://www.ncbi.nlm.nih.gov/nuccore/KX447512
Brazil/2015/ZBRC301 zika KY558995 2015-05-13 South America Brazil Brazil Brazil genbank genome Faria et al https://www.ncbi.nlm.nih.gov/nuccore/KY558995
Brazil/2015/ZBRA105 zika KY558989 2015-02-23 South America Brazil Brazil Brazil genbank genome Faria et al https://www.ncbi.nlm.nih.gov/nuccore/KY558989
Brazil/2016/ZBRC16 zika KY558991 2016-01-19 South America Brazil Brazil Brazil genbank genome Faria et al https://www.ncbi.nlm.nih.gov/nuccore/KY558991
V8375 zika KU501217 2015-11-01 North America Guatemala Guatemala Guatemala genbank genome Lanciotti et al https://www.ncbi.nlm.nih.gov/nuccore/KU501217
Nica1_16 zika KX421195 2016-01-19 North America Nicaragua Nicaragua Nicaragua genbank genome Tabata et al https://www.ncbi.nlm.nih.gov/nuccore/KX421195
Brazil/2015/ZBRC303 zika KY558997 2015-05-14 South America Brazil Brazil Brazil genbank genome Faria et al https://www.ncbi.nlm.nih.gov/nuccore/KY558997
SMGC_1 zika KX266255 2016-02-14 Oceania American Samoa American Samoa American Samoa genbank genome Bi et al https://www.ncbi.nlm.nih.gov/nuccore/KX266255
strain virus genbank_accession date region country division city db segment authors
PAN/CDC_259359_V1_V3/2015 zika KX156774 2015-12-18 North America Panama Panama Panama genbank genome Shabman et al
COL/FLR_00024/2015 zika MF574569 2015-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al
PRVABC59 zika KU501215 2015-12-XX North America Puerto Rico Puerto Rico Puerto Rico genbank genome Lanciotti et al
COL/FLR_00008/2015 zika MF574562 2015-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al
Colombia/2016/ZC204Se zika KY317939 2016-01-06 South America Colombia Colombia Colombia genbank genome Quick et al
ZKC2/2016 zika KX253996 2016-02-16 Oceania American Samoa American Samoa American Samoa genbank genome Wu et al
VEN/UF_1/2016 zika KX702400 2016-03-25 South America Venezuela Venezuela Venezuela genbank genome Blohm et al
DOM/2016/BB_0059 zika KY785425 2016-04-04 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al
BRA/2016/FC_6706 zika KY785433 2016-04-08 South America Brazil Brazil Brazil genbank genome Metsky et al
DOM/2016/BB_0183 zika KY785420 2016-04-18 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al
EcEs062_16 zika KX879603 2016-04-XX South America Ecuador Ecuador Ecuador genbank genome Marquez et al
HND/2016/HU_ME59 zika KY785418 2016-05-13 North America Honduras Honduras Honduras genbank genome Metsky et al
DOM/2016/MA_WGS16_011 zika KY785484 2016-06-06 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al
DOM/2016/BB_0433 zika KY785441 2016-06-13 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al
USA/2016/FL022 zika KY075935 2016-07-22 North America Usa Usa Usa genbank genome Grubaugh et al
SG_027 zika KY241697 2016-08-27 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al
SG_074 zika KY241744 2016-08-28 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al
SG_056 zika KY241726 2016-08-28 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al
USA/2016/FLUR022 zika KY325473 2016-08-31 North America Usa Usa Usa genbank genome Grubaugh et al
Aedes_aegypti/USA/2016/FL05 zika KY075937 2016-09-09 North America Usa Usa Usa genbank genome Grubaugh et al
SG_018 zika KY241688 2016-09-13 Southeast Asia Singapore Singapore Singapore genbank genome Ho et al
USA/2016/FLWB042 zika KY325478 2016-09-26 North America Usa Usa Usa genbank genome Grubaugh et al
COL/PRV_00028/2015 zika MF574578 2016-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al
Thailand/1610acTw zika MF692778 2016-10-XX Southeast Asia Thailand Thailand Thailand genbank genome Lin et al
1_0087_PF zika KX447509 2013-12-XX Oceania French Polynesia French Polynesia French Polynesia genbank genome Pettersson et al
1_0199_PF zika KX447519 2013-11-XX Oceania French Polynesia French Polynesia French Polynesia genbank genome Pettersson et al
1_0181_PF zika KX447512 2013-12-XX Oceania French Polynesia French Polynesia French Polynesia genbank genome Pettersson et al
Brazil/2015/ZBRC301 zika KY558995 2015-05-13 South America Brazil Brazil Brazil genbank genome Faria et al
Brazil/2015/ZBRA105 zika KY558989 2015-02-23 South America Brazil Brazil Brazil genbank genome Faria et al
Brazil/2016/ZBRC16 zika KY558991 2016-01-19 South America Brazil Brazil Brazil genbank genome Faria et al
V8375 zika KU501217 2015-11-01 North America Guatemala Guatemala Guatemala genbank genome Lanciotti et al
Nica1_16 zika KX421195 2016-01-19 North America Nicaragua Nicaragua Nicaragua genbank genome Tabata et al
Brazil/2015/ZBRC303 zika KY558997 2015-05-14 South America Brazil Brazil Brazil genbank genome Faria et al
SMGC_1 zika KX266255 2016-02-14 Oceania American Samoa American Samoa American Samoa genbank genome Bi et al
2 changes: 2 additions & 0 deletions phylogenetic/example_data/metadata_usvi.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
genbank_accession genbank_accession_rev accession strain date region country division location length host release_date update_date sra_accessions authors institution url
USVI/37/2016 VI37 USVI/37/2016 2016-10-06 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
Loading

0 comments on commit 870c938

Please sign in to comment.