Skip to content

Commit

Permalink
Append usvi data
Browse files Browse the repository at this point in the history
  • Loading branch information
@j23414
j23414 committed Nov 21, 2023
1 parent a53b5e4 commit 94b7590
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 94b7590

Please sign in to comment.