/Josh_Scripts

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Josh_Scripts

a summary of all scripts developed in MDU PHL

  • ChatGPT mdu_chatgpt.py (mdu_gpt)-- a trial app with free api from chatGPT (free plan end --need to buy a plan)

  • CIVET

    • build_db.py -- create a consensus db for CIVET HAV analysis
    • create_civet_command.py -- output civet command
    • create_consensus.py -- good command to create consensus for short sequence against with reference
    • civet.yml -- conda yml file for civet environment

  • compare_pipeline

    • mdu_compare.py -- using old version of bohra to compare two samples use listeria conda env to run
    • listeria.yml -- conda env for old bohra and mdu-listeria

  • CPA_report -- some CPA report draft/template

  • emmtyper

    • run_emm.py -- a command to run emmtyper with a list of contigs as input

  • Genome_SIZE_research -- research scripts and tables on genome size threshold

  • HAV -- scripts for HAV report

    • get_new_samples.py -- rename the tree leaves and get the new sample list for each serotype
    • hav_analysis.py -- blastn analyis on HAV new samples and build the tree for each serotype
    • hav_genotype.py -- typing hav sequences
    • hav_plot.r -- plot hav master tree and subtree with ggtree
    • QLD_hav.py -- clean up seqs shared from Queensland
    • hav.yml -- conda environment to run HAV analysis

  • josh_cluster -- a hierarchical clustering method with input matrix from Bohra

    • josh_cluster.py -- clustering script
    • josh_pca.py -- PCA plot and clustering
    • LS_reporting.yml -- conda environment with scikit-learn package

  • KMCP

    • mdu-kmcp-search.py -- run KMCP on mdu servers
    • result_summary.py -- summary results from KMCP
    • kmcp.yml -- conda environment to run KMCP

  • kraken_db_download

    • db_download.py -- download fasta file with id
    • db_download.yml -- conda environment with efetch/esearch

  • MTB -- MTB report scripts

    • add_PHESS.py -- add PHESS ID to amr table
    • make_change.py -- make change in the MTB cluster db
    • merge_cluster_db.py -- merge cluster names for different lineages
    • mtb_new_process.py -- cleptr analysis
    • MTB_new_report.py -- create report tree/files/pngs
    • remove_dup.py -- remove duplicates in MTB cluster db
    • remove_samples.py -- remove samples from MTB cluster db
    • templete_fit.py -- create doc report
    • MTB_reporting.yml -- conda environment for MTB_new_report.py and templete_fit.py

  • nextflow_clean (Danger)

    • nextflow_clean.py -- clean up large files in nextflow folder Do not use this -- will crush servers

  • ONT_research

    • mdu-ont.py -- same as mdu ont

  • PTP -- scripts for Monkey pox virus PTP

    • create_consensus.py -- create consensus with reference
    • reads_stats.py -- filter species/domain/human reads in metagenomics seqs using kraken2 and taxonkit
    • run_abricate.py -- run abricate on reads
    • sep_ref.py -- break large refs to single contigs fasta

  • salmonella

    • salmonella_report.py -- Original STE reporting code

  • scripts -- collection of quick scripts

    • bad_symlink_cleaner.py -- clean up bad symlinks
    • copy_contigs_for_mashtree.py -- copy/symlink contigs for input of mashtree
    • cp_share.py -- copy reads for mdu share
    • find_the_close_samples.py -- very useful to list number of samples to include in bohra analysis. need pandas in envronment
    • json_to_csv.py -- quick tools to transfer json files to csv
    • nwktojson.py -- quick tools to transfer nwk files to json
    • remove_samples_from_cgmlst.py -- remove samples from cgmlst db to rerun qc finalise step (with cgmlst)
    • sra_download.py -- download reads with SRA ids from NCBI
    • which_run.py -- search mdu id in the /home/mdu/instruments/

  • Shigella

    • create_shigs_input.py -- create input files for mdu_shigs.py
    • create_sonnei_summary.py -- create report summary
    • mdu_mykrobe.py -- run mykrobe
    • mdu_shigs.py -- shigella analysis with input from create_shigs_input.py
    • shigella.yml -- conda environment to run mdu_shigs.py
    • Sonnei_tree.Rmd -- R Markdown to build sonnei trees
    • sonneityping_with_shigs.py -- typing with shigs results

  • SKA

    • run_ska.py -- run SKA with a tab file as input

  • STE_report

    • cgT_db.py -- checking cgT db
    • STE_summary.py -- create summary on recent cgTs
    • run_bohra.py -- run bohra analysis on each cgTs
    • cp_bohra_links.py -- publish bohra links

  • streptyping -- Strep pnemo typing with shore seqs

    • mdu-streptyping.py -- typing Strep pnemo using blastn (fasta as input)
    • strep_consensus.py -- create consensus for typing

Author Jianshu Zhang

Email: josh.zhang@unimelb.edu.au / zjs0317@gmail.com