SUMMARY

This folder is a package that contains scripts and files for running three experiments: mapping of H1N1 sequences from human, swine, and birds to California/07/2009 (H1N1); mapping of Perth/16/2009 to itself at varing levels of divergence; pairwise mapping of influenza A sequences with and without VAPOR pre-classification.

REQUIREMENTS

The following are required, and where applicable must be in your PATH:
    Minimap2 2.12
    BWA 0.7.17
    Hisat2 v2.1.0
    NGM 0.5.0
    VAPOR 0.1
    Python3.x
    GNU Parallel 20160222

Additionally, artificialFastqGenerator (afg) v1.0.0 must be placed in code/afg 

Additionally, the following resources are required:

res/: a set of used resources with the following files and their respective indices for BWA, NGM, and HiSAT2.
    HA_A_allsp_nfu.fa
    perth1609.fa
    cali0709.fa
    HA_AvH1N1_nf.fa
    HA_HuH1N1_nf.fa
    HA_SwH1N1_nf.fa

This can be downloaded as the tar archive https://s3.climb.ac.uk/vapor-benchmark-data/benchmarking_mapping_res_20_12_18.tar.gz

For plotting, pandas 0.23.4, matplotlib 2.2.3, NumPy 1.15.2, and seaborn 0.9.0 are required.

USAGE

For the Perth mutation and mapping experiment run:

    parallel --jobs N < code/parallel_commands/perth.pcom.sh > logs/perth.pcom.log 2>&1
    bash code/fetch_perth_results.sh > HA_Perth1609vsPerth1609_mutall.csv
    python3 plotting/plot_boxes_mutation_perth.py HA_Perth1609vsPerth1609_mutall.csv

For the zoonotic segment mapping experiment, run:

    parallel --jobs N < code/parallel_commands/H1N1.pcom.sh > logs/H1N1.pcom.log 2>&1
    cat results_H1N1/HA_HuH1N1vsCali0709*.csv  > HA_HuH1N1vsCali0709.csv 
    cat results_H1N1/HA_AvH1N1vsCali0709*.csv  > HA_AvH1N1vsCali0709.csv 
    cat results_H1N1/HA_SwH1N1vsCali0709*.csv  > HA_SwH1N1vsCali0709.csv 
    python3 plotting/plot_zoo_hists.py HA_HuH1N1vsCali0709.csv HA_SwH1N1vsCali0709.csv HA_AvH1N1vsCali0709.csv

For the HA mapping without vapor, run:

    parallel --jobs N < code/parallel_commands/HA_basic.pcom.sh > logs/HA_basic.pcom.log 2>&1
    cat results_HA_basic/HA_basic*.csv > HA_basic.csv
    python3 plotting/plot_HA_basic_hexbins.py HA_basic.csv HA_hex_novapor.pdf

For the HA mapping with vapor, run:

    parallel --jobs N < code/parallel_commands/HA_basic_with_vapor.pcom.sh > logs/HA_basic_with_vapor.pcom.log 2>&1
    cat results_HA_basic_vapor/HA_basic_with_vapor*.csv > HA_basic_with_vapor.csv
    python3 plotting/plot_HA_basic_hexbins.py HA_basic_with_vapor.csv HA_hex_with_vapor.pdf