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isabeljoiaisabeljoia
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insert epitope information into workflow
1 parent 032ea5d commit cb85df3

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17 files changed

+1308
-124
lines changed

17 files changed

+1308
-124
lines changed

‎Snakefile

Lines changed: 24 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -1,45 +1,55 @@
1+
import pandas as pd
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configfile: "config/configfile.yaml"
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wildcard_constraints:
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a_or_b = r"a|b"
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a_or_b=r"a|b",
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9+
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build_dir = "results"
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auspice_dir = "auspice"
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distance_map_config = pd.read_table("config/distance_maps.tsv")
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build_dir = 'results'
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auspice_dir = 'auspice'
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rule all:
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input:
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expand("auspice/rsv_{subtype}_{build}_{resolution}.json",
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subtype = config.get("subtypes",['a']),
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build = config.get("builds_to_run", ['genome']),
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resolution = config.get("resolutions_to_run", ["all-time"])),
18+
expand(
19+
"auspice/rsv_{subtype}_{build}_{resolution}.json",
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subtype=config.get("subtypes", ["a"]),
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build=config.get("builds_to_run", ["genome"]),
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resolution=config.get("resolutions_to_run", ["all-time"]),
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),
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include: "workflow/snakemake_rules/chores.smk"
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include: "workflow/snakemake_rules/core.smk"
26+
# include: "workflow/snakemake_rules/chores.smk"
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include: "workflow/snakemake_rules/export.smk"
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29+
include: "workflow/snakemake_rules/core.smk"
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include: "workflow/snakemake_rules/export.smk"
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include: "workflow/snakemake_rules/download.smk"
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include: "workflow/snakemake_rules/glycosylation.smk"
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include: "workflow/snakemake_rules/clades.smk"
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if "deploy_url" in config:
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include: "workflow/snakemake_rules/nextstrain_automation.smk"
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rule clean:
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params:
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targets = ["auspice", "results"]
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targets=["auspice", "results"],
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shell:
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"""
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rm -rf {params.targets}
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"""
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rule clobber:
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params:
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targets = ["data", "auspice", "results"]
52+
targets=["data", "auspice", "results"],
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shell:
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"""
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rm -rf {params.targets}

‎config/auspice_config.json

Lines changed: 61 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,14 @@
11
{
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"title": "Genomic epidemiology of RSV",
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"maintainers": [
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{"name": "Laura Urbanska", "url": "http://nextstrain.org"},
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{"name": "Richard Neher", "url": "http://nextstrain.org"}
6-
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{
5+
"name": "Laura Urbanska",
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"url": "http://nextstrain.org"
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},
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{
9+
"name": "Richard Neher",
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"url": "http://nextstrain.org"
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}
712
],
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"data_provenance": [
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{
@@ -12,7 +17,6 @@
1217
}
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],
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"build_url": "https://github.com/nextstrain/rsv",
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"colorings": [
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{
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"key": "gt",
@@ -38,24 +42,70 @@
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"key": "glyc",
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"title": "Glycosylation",
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"type": "ordinal"
41-
} ],
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},
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{
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"key": "epi_00",
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"title": "Epitope 0",
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"type": "continuous"
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},
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{
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"key": "epi_01",
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"title": "Epitope 1",
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"type": "continuous"
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},
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{
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"key": "epi_02",
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"title": "Epitope 2",
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"type": "continuous"
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},
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{
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"key": "epi_03",
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"title": "Epitope 3",
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"type": "continuous"
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},
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{
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"key": "epi_04",
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"title": "Epitope 4",
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"type": "continuous"
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},
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{
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"key": "epi_05",
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"title": "Epitope 5",
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"type": "continuous"
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},
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{
77+
"key": "epi_all",
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"title": "All Epitopes",
79+
"type": "continuous"
80+
},
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{
82+
"key": "surface_residues_postf",
83+
"title": "Postfusion Surface Residues",
84+
"type": "continuous"
85+
},
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{
87+
"key": "surface_residues_pref",
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"title": "Prefusion Surface Residues",
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"type": "continuous"
90+
}
91+
],
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"geo_resolutions": [
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"country",
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"region"
4595
],
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"panels": [
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"tree",
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"map",
49-
"entropy"
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"tree",
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"map",
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"entropy"
50100
],
51101
"display_defaults": {
52102
"map_triplicate": true,
53-
"color_by" : "clade_membership",
103+
"color_by": "clade_membership",
54104
"transmission_lines": false
55-
},
105+
},
56106
"filters": [
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"country",
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"region",
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"clade_membership"
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]
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}
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}

‎config/configfile.yaml

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@@ -53,6 +53,11 @@ refine:
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ancestral:
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inference: "joint"
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cds:
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F: "F"
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G: "G"
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genome: "F"
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traits:
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columns: "country"
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‎config/distance_maps.tsv

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a_or_b build_name resolution compare_to attribute distance_map
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a F all-time root epi_00 epi_00
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a F all-time root epi_01 epi_01
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a F all-time root epi_02 epi_02
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a F all-time root epi_03 epi_03
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a F all-time root epi_04 epi_04
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a F all-time root epi_05 epi_05
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a F all-time root epi_all epi_all
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a F all-time root surface_residues_postf surface_residues_postf
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a F all-time root surface_residues_pref surface_residues_pref
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b F all-time root epi_00 epi_00
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b F all-time root epi_01 epi_01
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b F all-time root epi_02 epi_02
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b F all-time root epi_03 epi_03
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b F all-time root epi_04 epi_04
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b F all-time root epi_05 epi_05
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b F all-time root epi_all epi_all
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b F all-time root surface_residues_postf surface_residues_postf
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b F all-time root surface_residues_pref surface_residues_pref
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a F 3y root epi_00 epi_00
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a F 3y root epi_01 epi_01
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a F 3y root epi_02 epi_02
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a F 3y root epi_03 epi_03
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a F 3y root epi_04 epi_04
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a F 3y root epi_05 epi_05
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a F 3y root epi_all epi_all
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a F 3y root surface_residues_postf surface_residues_postf
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a F 3y root surface_residues_pref surface_residues_pref
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b F 3y root epi_00 epi_00
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b F 3y root epi_01 epi_01
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b F 3y root epi_02 epi_02
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b F 3y root epi_03 epi_03
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b F 3y root epi_04 epi_04
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b F 3y root epi_05 epi_05
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b F 3y root epi_all epi_all
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b F 3y root surface_residues_postf surface_residues_postf
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b F 3y root surface_residues_pref surface_residues_pref
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a F 6y root epi_00 epi_00
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a F 6y root epi_01 epi_01
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a F 6y root epi_02 epi_02
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a F 6y root epi_03 epi_03
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a F 6y root epi_04 epi_04
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a F 6y root epi_05 epi_05
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a F 6y root epi_all epi_all
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a F 6y root surface_residues_postf surface_residues_postf
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a F 6y root surface_residues_pref surface_residues_pref
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b F 6y root epi_00 epi_00
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b F 6y root epi_01 epi_01
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b F 6y root epi_02 epi_02
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b F 6y root epi_03 epi_03
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b F 6y root epi_04 epi_04
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b F 6y root epi_05 epi_05
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b F 6y root epi_all epi_all
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b F 6y root surface_residues_postf surface_residues_postf
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b F 6y root surface_residues_pref surface_residues_pref
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‎config/distance_maps/F/epi_00.json

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{
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"default": 0,
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"map": {
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"F": {
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"62": 1,
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"63": 1,
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"64": 1,
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"65": 1,
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"66": 1,
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"67": 1,
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"68": 1,
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"69": 1,
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"196": 1,
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"197": 1,
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"198": 1,
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"199": 1,
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"200": 1,
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"201": 1,
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"202": 1,
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"203": 1,
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"204": 1,
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"205": 1,
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"206": 1,
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"207": 1,
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"208": 1,
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"209": 1,
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"210": 1
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}
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},
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"name": "epi_00"
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}

‎config/distance_maps/F/epi_01.json

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{
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"default": 0,
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"map": {
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"F": {
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"31": 1,
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"378": 1,
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"344": 1,
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"380": 1
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}
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},
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"name": "epi_01"
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}

‎config/distance_maps/F/epi_02.json

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{
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"default": 0,
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"map": {
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"F": {
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"254": 1,
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"255": 1,
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"256": 1,
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"257": 1,
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"258": 1,
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"259": 1,
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"260": 1,
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"261": 1,
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"262": 1,
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"263": 1,
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"264": 1,
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"265": 1,
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"266": 1,
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"267": 1,
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"269": 1,
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"270": 1,
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"272": 1,
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"273": 1,
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"274": 1,
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"275": 1,
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"276": 1,
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"277": 1
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}
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},
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"name": "epi_02"
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}

‎config/distance_maps/F/epi_03.json

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{
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"default": 0,
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"map": {
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"F": {
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"44": 1,
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"45": 1,
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"46": 1,
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"47": 1,
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"309": 1,
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}
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},
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"name": "epi_03"
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}

‎config/distance_maps/F/epi_04.json

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{
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"default": 0,
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"map": {
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"F": {
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"422": 1,
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"423": 1,
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"424": 1,
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"425": 1,
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"426": 1,
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"434": 1,
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"435": 1,
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"436": 1
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}
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},
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"name": "epi_04"
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}

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