Zika-Virus-Re

This is the repository of scripts done to calculate the Re of the Zika Virus across time.

ALL SCRIPTS ARE LOCATED IN scripts/ UNLESS OTHERWISE SPECIFIED

getting the data + metadata

Query: "esearch -db nucleotide -query 'txid64320[Organism] AND complete[Title] AND 9000:12000[slen]' | efetch -format gb > zika.gb"

• output zika.gb

Parse into fasta

• command: python3 parse_genbank.py zika.gb zika_meta.csv zika.fa
• input: gb from genbank query
• output zika.fa, zika_meta.csv # opted not to use this metadata data in favour of bioplus/get_metadata.py

Get metadata

• command python3 /Bioplus/Bioplus/get_metadata.py zika.fa --email wwang859@uwo.ca -o zika_metadata.csv
• input: raw fasta from database
• output: zika_metadata.csv

Move all three files into files/raw

• zika_metadata.csv, zika.fa, zika.gb

cleaning data

add dates to sequences

• command: python3 /Bioplus/Bioplus/add_dates.py zika.fa zika_metadata.csv > zika_dates.fa
• input: zika.fasta # raw fasta
• output: zika_dates.fa

remove ambiguous sequences

• command: python3 remove_ambigous_sequences.py
• input: zika_dates.fa
• output: zika_clean_dates.fa

downsample

• command: python3 scripts/downsample.py
• input: zika_clean_dates.fa
• ouput: zika_downsample.fa

align to find who to clean out as outlier

• command: mafft --auto zika_downsample.fa > first_aln.fa
• input: zika_downsample.fa
• output: first_aln.fa

remove outlier sequences which introduced gaps

• command: python3 scripts/remove_outlier_sequences.py
• input: zika_downsample.fa
• output: zika_no_out.fa

Move cleaning-progress files to files/cleaning

• zika_dates.fa, zika_clean_dates.fa, zia_aln.fa, zika_no_out.fa

make final files for BEAST2

change to decimal years for BEAST2

• command python3 change_dec_year.py zika_no_out.fa zika_final.fa
• inputL zika_no_out.fa
• output: zika_final.fa

realign for beast2 and iqtree

• mafft python3 zika_final.fa > zika_aln.fa

filter metadata to match these final sequences

• python3 filter_metadata.csv
• input: zika.fa, zika_metadata.csv
• output: zika_metadata_final.csv

Move final files for analysis into files/final

• zika_final.fa, zika_aln.fa, zika_metadata_final.csv

IQTREE

do this for beast2 starting tree

• command: iqtree2 -m MFP --threads 32 -s zika_aln.fa

Move all output files to iqtree/

BEAST

all files are located in beast/run*

Generating figures

All figures are uploaded to figures/

I used tracer on my local machine

• posterior.pdf is the combined trace

The server couldn't run scripts/bdsky_plot_1.3.3.R on the server because of dependency issues, ran it locally instead

• generated skyline_plot.pdf

I used figtree to generate the trees, and photopea.com (online photoshop) to merge them together on my local machine

• original.png is the ML tree produced by iqtree2
• run1.png is the tree output from BEAST2 run1
• run2.png is the tree output from BREAST2 run2