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Snakefile
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Snakefile
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rule all:
input:
auspice_tree = "auspice/mers_tree.json",
auspice_meta = "auspice/mers_meta.json"
rule files:
params:
input_fasta = "data/mers.fasta",
dropped_strains = "config/dropped_strains.txt",
reference = "config/mers_reference.gb",
#colors = "config/colors.tsv",
auspice_config = "config/auspice_config.json"
files = rules.files.params
rule download:
message: "Downloading sequences from fauna"
output:
sequences = "data/mers.fasta"
params:
fasta_fields = "strain virus accession collection_date region country division location source locus authors url title journal puburl"
shell:
"""
python3 ../fauna/vdb/download.py \
--database vdb \
--virus mers \
--fasta_fields {params.fasta_fields} \
--resolve_method choose_genbank \
--path $(dirname {output.sequences}) \
--fstem $(basename {output.sequences} .fasta)
"""
rule parse:
message: "Parsing fasta into sequences and metadata"
input:
sequences = rules.download.output.sequences
output:
sequences = "results/sequences.fasta",
metadata = "results/metadata.tsv"
params:
fasta_fields = "strain virus accession date region country division city db segment authors url title journal paper_url"
shell:
"""
augur parse \
--sequences {input.sequences} \
--output-sequences {output.sequences} \
--output-metadata {output.metadata} \
--fields {params.fasta_fields}
"""
rule filter:
message:
"""
Filtering to
- {params.sequences_per_group} sequence(s) per {params.group_by!s}
- from {params.min_date} onwards
- excluding strains in {input.exclude}
- minimum genome length of {params.min_length} (50% of Mers virus genome)
"""
input:
sequences = rules.parse.output.sequences,
metadata = rules.parse.output.metadata,
exclude = files.dropped_strains
output:
sequences = "results/filtered.fasta"
params:
group_by = "country year month",
sequences_per_group = 1,
min_date = 2012,
min_length = 5385
shell:
"""
augur filter \
--sequences {input.sequences} \
--metadata {input.metadata} \
--exclude {input.exclude} \
--output {output.sequences} \
--group-by {params.group_by} \
--sequences-per-group {params.sequences_per_group} \
--min-date {params.min_date} \
--min-length {params.min_length}
"""
rule align:
message:
"""
Aligning sequences to {input.reference}
- filling gaps with N
"""
input:
sequences = rules.filter.output.sequences,
reference = files.reference
output:
alignment = "results/aligned.fasta"
shell:
"""
augur align \
--sequences {input.sequences} \
--reference-sequence {input.reference} \
--output {output.alignment} \
--fill-gaps \
--remove-reference
"""
rule tree:
message: "Building tree"
input:
alignment = rules.align.output.alignment
output:
tree = "results/tree_raw.nwk"
shell:
"""
augur tree \
--alignment {input.alignment} \
--output {output.tree}
"""
rule refine:
message:
"""
Refining tree
- estimate timetree
- use {params.coalescent} coalescent timescale
- estimate {params.date_inference} node dates
- filter tips more than {params.clock_filter_iqd} IQDs from clock expectation
"""
input:
tree = rules.tree.output.tree,
alignment = rules.align.output,
metadata = rules.parse.output.metadata
output:
tree = "results/tree.nwk",
node_data = "results/branch_lengths.json"
params:
coalescent = "opt",
date_inference = "marginal",
clock_filter_iqd = 4
shell:
"""
augur refine \
--tree {input.tree} \
--alignment {input.alignment} \
--metadata {input.metadata} \
--output-tree {output.tree} \
--output-node-data {output.node_data} \
--timetree \
--coalescent {params.coalescent} \
--date-confidence \
--date-inference {params.date_inference} \
--clock-filter-iqd {params.clock_filter_iqd}
"""
rule ancestral:
message: "Reconstructing ancestral sequences and mutations"
input:
tree = rules.refine.output.tree,
alignment = rules.align.output
output:
node_data = "results/nt_muts.json"
params:
inference = "joint"
shell:
"""
augur ancestral \
--tree {input.tree} \
--alignment {input.alignment} \
--output {output.node_data} \
--inference {params.inference}
"""
rule translate:
message: "Translating amino acid sequences"
input:
tree = rules.refine.output.tree,
node_data = rules.ancestral.output.node_data,
reference = files.reference
output:
node_data = "results/aa_muts.json"
shell:
"""
augur translate \
--tree {input.tree} \
--ancestral-sequences {input.node_data} \
--reference-sequence {input.reference} \
--output {output.node_data} \
"""
rule traits:
message:
"""
Inferring ancestral traits for {params.columns!s}
- increase uncertainty of reconstruction by {params.sampling_bias_correction} to partially account for sampling bias
"""
input:
tree = rules.refine.output.tree,
metadata = rules.parse.output.metadata
output:
node_data = "results/traits.json",
params:
columns = "region country",
sampling_bias_correction = 3
shell:
"""
augur traits \
--tree {input.tree} \
--metadata {input.metadata} \
--output {output.node_data} \
--columns {params.columns} \
--confidence \
--sampling-bias-correction {params.sampling_bias_correction}
"""
rule export:
message: "Exporting data files for for auspice"
input:
tree = rules.refine.output.tree,
metadata = rules.parse.output.metadata,
branch_lengths = rules.refine.output.node_data,
traits = rules.traits.output.node_data,
nt_muts = rules.ancestral.output.node_data,
aa_muts = rules.translate.output.node_data,
#colors = files.colors,
auspice_config = files.auspice_config
output:
auspice_tree = rules.all.input.auspice_tree,
auspice_meta = rules.all.input.auspice_meta
shell:
"""
augur export \
--tree {input.tree} \
--metadata {input.metadata} \
--node-data {input.branch_lengths} {input.traits} {input.nt_muts} {input.aa_muts} \
--auspice-config {input.auspice_config} \
--output-tree {output.auspice_tree} \
--output-meta {output.auspice_meta}
"""
rule clean:
message: "Removing directories: {params}"
params:
"results ",
"auspice"
shell:
"rm -rfv {params}"