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: [email protected] / [email protected]