config.yaml

Linux:
  Default:
    Analysis:
      PWM number of sequence threshold: 5
      TF MSA path: example_data/mutation_analysis/artificial/TF_MSA.fasta
      TFBS path: example_data/mutation_analysis/artificial/TFBS.tsv
      TFBS random mutations: 15
      gene path: example_data/mutation_analysis/artificial/genes.tsv
      genes of interest (name long): genes of interest
      genes of interest (name short): GoI
      interest path: example_data/mutation_analysis/artificial/genes_of_interest.tsv
      mutation path: example_data/mutation_analysis/artificial/mutations.tsv
      other genes (name long): other genes
      other genes (name short): other
      output directory: results/mutation_analysis/
      protein domain path: example_data/mutation_analysis/artificial/domains.tsv
      regulation path: example_data/mutation_analysis/artificial/regulation.tsv
      relative promoter start: -100
      substitution matrix path: substitution_matrices/PAM10.tsv
    NGS:
      BWA executable: /usr/bin/bwa
      SAMTools executable: /usr/bin/samtools
      VarScan executable: /usr/bin/varscan
      output directory: results/NGS/
      p-value: 0.05
      quality control cut-off: 30
      reads directory: example_data/NGS/reads
      reference genome path: example_data/NGS/ref_genome.fasta
    PATRIC:
      input file: example_data/PATRIC/resistance.csv
      output file: results/PATRIC/resistance.tsv
    RegulonDB:
      TF MSA input: example_data/regulonDB/artificial_TF_MSA.txt
      TF-TF input: example_data/regulonDB/artificial_TF_TF.tsv
      TF-TU input: example_data/regulonDB/artificial_TF_TU.tsv
      TF-gene input: example_data/regulonDB/artificial_TF_gene.tsv
      TF-operon input: example_data/regulonDB/artificial_TF_operon.tsv
      TFBS input: example_data/regulonDB/artificial_TFBS.tsv
      TU input: example_data/regulonDB/artificial_TUs.tsv
      gene input: example_data/regulonDB/artificial_genes.tsv
      operon input: example_data/regulonDB/artificial_operons.tsv
      output directory: results/regulonDB/
      promoter input: example_data/regulonDB/artificial_promoters.tsv
    UniProt:
      input file: example_data/UniProt/s_aureus_domains_shortened.txt
      output file: results/UniProt/domains.tsv
    VCF Merger:
      input directory: example_data/vcf_merger/
      output file: results/vcf_merger/mutation.tsv
  GUI:
    colours:
      description text: '#4F81BD'
      description title: '#4F81BD'
      section title: '#C0504D'
      sub-section title: '#76923D'
    fonts:
      check button:
      - Calibri
      - 10
      description text:
      - Calibri
      - 10
      description title:
      - Calibri
      - 14
      - bold
      entry field label:
      - Calibri
      - 10
      entry field text:
      - Calibri
      - 9
      file chooser button:
      - Calibri
      - 9
      run button:
      - Calibri
      - 9
      section title:
      - Calibri
      - 14
      - bold
      status line:
      - Calibri
      - 10
      sub-section title:
      - Calibri
      - 10
      - bold
    heights:
      description frame: 250
    styles:
      theme: clam
    widths:
      description frame: 400
      description text: 390
      file/directory chooser button: 3
      file/directory entry field: 30
      left settings button: 15
      number entry field: 15
      right settings button: 15
      run button: 20
      save/cancel button: 15
      separator line width: 1
      status box: 50
      status box border: 1
    x-margins:
      column: 20
      description text:
      - 0
      - 0
      description title:
      - 0
      - 0
      empty check button:
      - 10
      - 0
      entry field label:
      - 0
      - 10
      entry field text:
      - 0
      - 0
      file chooser button:
      - 0
      - 0
      left settings button:
      - 0
      - 0
      right settings button:
      - 0
      - 0
      run button:
      - 0
      - 0
      section title:
      - 0
      - 0
      separator:
      - 0
      - 0
      status box frame:
      - 0
      - 0
      subsection title:
      - 0
      - 0
      text check button:
      - 0
      - 0
      text separator:
      - 0
      - 0
      window left: 5
      window right: 10
    y-margins:
      column:
      - 0
      - 0
      description text:
      - 0
      - 0
      description title:
      - 15
      - 0
      empty check button:
      - 0
      - 0
      entry field label:
      - 0
      - 0
      entry field text:
      - 2
      - 2
      field name:
      - 0
      - 0
      file chooser button:
      - 0
      - 0
      left settings button:
      - 0
      - 0
      right settings button:
      - 0
      - 0
      run button:
      - 0
      - 0
      section title:
      - 15
      - 0
      separator:
      - 10
      - 10
      status box frame:
      - 0
      - 0
      subsection title:
      - 0
      - 0
      text check button:
      - 0
      - 0
      text separator:
      - 0
      - 0
      window bottom: 10
  User:
    Analysis:
      PWM number of sequence threshold: 5
      TF MSA path: example_data/mutation_analysis/artificial/TF_MSA.fasta
      TFBS path: example_data/mutation_analysis/artificial/TFBS.tsv
      TFBS random mutations: 15
      gene path: example_data/mutation_analysis/artificial/genes.tsv
      genes of interest (name long): genes of interest
      genes of interest (name short): GoI
      interest path: example_data/mutation_analysis/artificial/genes_of_interest.tsv
      mutation path: example_data/mutation_analysis/artificial/mutations.tsv
      other genes (name long): other genes
      other genes (name short): other
      output directory: results/mutation_analysis/
      protein domain path: example_data/mutation_analysis/artificial/domains.tsv
      regulation path: example_data/mutation_analysis/artificial/regulation.tsv
      relative promoter start: -100
      substitution matrix path: substitution_matrices/PAM10.tsv
    NGS:
      BWA executable: /usr/bin/bwa
      SAMTools executable: /usr/bin/samtools
      VarScan executable: /usr/bin/varscan
      output directory: results/NGS/
      p-value: 0.05
      quality control cut-off: 30
      reads directory: example_data/NGS/reads
      reference genome path: example_data/NGS/ref_genome.fasta
    PATRIC:
      input file: example_data/PATRIC/resistance.csv
      output file: results/PATRIC/resistance.tsv
    RegulonDB:
      TF MSA input: example_data/regulonDB/artificial_TF_MSA.txt
      TF-TF input: example_data/regulonDB/artificial_TF_TF.tsv
      TF-TU input: example_data/regulonDB/artificial_TF_TU.tsv
      TF-gene input: example_data/regulonDB/artificial_TF_gene.tsv
      TF-operon input: example_data/regulonDB/artificial_TF_operon.tsv
      TFBS input: example_data/regulonDB/artificial_TFBS.tsv
      TU input: example_data/regulonDB/artificial_TUs.tsv
      gene input: example_data/regulonDB/artificial_genes.tsv
      operon input: example_data/regulonDB/artificial_operons.tsv
      output directory: results/regulonDB/
      promoter input: example_data/regulonDB/artificial_promoters.tsv
    UniProt:
      input file: example_data/UniProt/s_aureus_domains_shortened.txt
      output file: results/UniProt/domains.tsv
    VCF Merger:
      input directory: example_data/vcf_merger/
      output file: results/vcf_merger/mutation.tsv
Mac OS X:
  Default:
    Analysis:
      PWM number of sequence threshold: 5
      TF MSA path: example_data/mutation_analysis/artificial/TF_MSA.fasta
      TFBS path: example_data/mutation_analysis/artificial/TFBS.tsv
      TFBS random mutations: 15
      gene path: example_data/mutation_analysis/artificial/genes.tsv
      genes of interest (name long): genes of interest
      genes of interest (name short): GoI
      interest path: example_data/mutation_analysis/artificial/genes_of_interest.tsv
      mutation path: example_data/mutation_analysis/artificial/mutations.tsv
      other genes (name long): other genes
      other genes (name short): other
      output directory: results/mutation_analysis/
      protein domain path: example_data/mutation_analysis/artificial/domains.tsv
      regulation path: example_data/mutation_analysis/artificial/regulation.tsv
      relative promoter start: -100
      substitution matrix path: substitution_matrices/PAM10.tsv
    NGS:
      BWA executable: /usr/bin/bwa
      SAMTools executable: /usr/bin/samtools
      VarScan executable: /usr/bin/varscan
      output directory: results/NGS/
      p-value: 0.05
      quality control cut-off: 30
      reads directory: example_data/NGS/reads
      reference genome path: example_data/NGS/ref_genome.fasta
    PATRIC:
      input file: example_data/PATRIC/resistance.csv
      output file: results/PATRIC/resistance.tsv
    RegulonDB:
      TF MSA input: example_data/regulonDB/artificial_TF_MSA.txt
      TF-TF input: example_data/regulonDB/artificial_TF_TF.tsv
      TF-TU input: example_data/regulonDB/artificial_TF_TU.tsv
      TF-gene input: example_data/regulonDB/artificial_TF_gene.tsv
      TF-operon input: example_data/regulonDB/artificial_TF_operon.tsv
      TFBS input: example_data/regulonDB/artificial_TFBS.tsv
      TU input: example_data/regulonDB/artificial_TUs.tsv
      gene input: example_data/regulonDB/artificial_genes.tsv
      operon input: example_data/regulonDB/artificial_operons.tsv
      output directory: results/regulonDB/
      promoter input: example_data/regulonDB/artificial_promoters.tsv
    UniProt:
      input file: example_data/UniProt/s_aureus_domains_shortened.txt
      output file: results/UniProt/domains.tsv
    VCF Merger:
      input directory: example_data/vcf_merger/
      output file: results/vcf_merger/mutation.tsv
  GUI:
    colours:
      description text: '#4F81BD'
      description title: '#4F81BD'
      section title: '#C0504D'
      sub-section title: '#76923D'
    fonts:
      check button:
      - Calibri
      - 12
      description text:
      - Calibri
      - 12
      description title:
      - Calibri
      - 16
      - bold
      entry field label:
      - Calibri
      - 12
      entry field text:
      - Calibri
      - 10
      file chooser button:
      - Calibri
      - 12
      run button:
      - Calibri
      - 12
      section title:
      - Calibri
      - 16
      - bold
      status line:
      - Calibri
      - 12
      sub-section title:
      - Calibri
      - 12
      - bold
    heights:
      description frame: 210
    styles:
      theme: aqua
    widths:
      description frame: 400
      description text: 390
      file/directory chooser button: 3
      file/directory entry field: 30
      left settings button: 15
      number entry field: 15
      right settings button: 15
      run button: 20
      save/cancel button: 15
      separator line width: 1
      status box: 50
      status box border: 1
    x-margins:
      column: 20
      description text:
      - 0
      - 0
      description title:
      - 0
      - 0
      empty check button:
      - 10
      - 0
      entry field label:
      - 0
      - 10
      entry field text:
      - 0
      - 0
      file chooser button:
      - 0
      - 0
      left settings button:
      - 0
      - 0
      right settings button:
      - 0
      - 0
      run button:
      - 0
      - 0
      section title:
      - 0
      - 0
      separator:
      - 0
      - 0
      status box frame:
      - 0
      - 0
      subsection title:
      - 0
      - 0
      text check button:
      - 0
      - 0
      text separator:
      - 0
      - 0
      window left: 5
      window right: 10
    y-margins:
      column:
      - 0
      - 0
      description text:
      - 0
      - 0
      description title:
      - 15
      - 0
      empty check button:
      - 0
      - 0
      entry field label:
      - 0
      - 0
      entry field text:
      - 2
      - 2
      field name:
      - 0
      - 0
      file chooser button:
      - 0
      - 0
      left settings button:
      - 0
      - 0
      right settings button:
      - 0
      - 0
      run button:
      - 0
      - 0
      section title:
      - 15
      - 0
      separator:
      - 10
      - 10
      status box frame:
      - 0
      - 0
      subsection title:
      - 0
      - 0
      text check button:
      - 0
      - 0
      text separator:
      - 0
      - 0
      window bottom: 20
  User:
    Analysis:
      PWM number of sequence threshold: 5
      TF MSA path: example_data/mutation_analysis/artificial/TF_MSA.fasta
      TFBS path: example_data/mutation_analysis/artificial/TFBS.tsv
      TFBS random mutations: 15
      gene path: example_data/mutation_analysis/artificial/genes.tsv
      genes of interest (name long): genes of interest
      genes of interest (name short): GoI
      interest path: example_data/mutation_analysis/artificial/genes_of_interest.tsv
      mutation path: example_data/mutation_analysis/artificial/mutations.tsv
      other genes (name long): other genes
      other genes (name short): other
      output directory: results/mutation_analysis/
      protein domain path: example_data/mutation_analysis/artificial/domains.tsv
      regulation path: example_data/mutation_analysis/artificial/regulation.tsv
      relative promoter start: -100
      substitution matrix path: substitution_matrices/PAM10.tsv
    NGS:
      BWA executable: /usr/bin/bwa
      SAMTools executable: /usr/bin/samtools
      VarScan executable: /usr/bin/varscan
      output directory: results/NGS/
      p-value: 0.05
      quality control cut-off: 30
      reads directory: example_data/NGS/reads
      reference genome path: example_data/NGS/ref_genome.fasta
    PATRIC:
      input file: example_data/PATRIC/resistance.csv
      output file: results/PATRIC/resistance.tsv
    RegulonDB:
      TF MSA input: example_data/regulonDB/artificial_TF_MSA.txt
      TF-TF input: example_data/regulonDB/artificial_TF_TF.tsv
      TF-TU input: example_data/regulonDB/artificial_TF_TU.tsv
      TF-gene input: example_data/regulonDB/artificial_TF_gene.tsv
      TF-operon input: example_data/regulonDB/artificial_TF_operon.tsv
      TFBS input: example_data/regulonDB/artificial_TFBS.tsv
      TU input: example_data/regulonDB/artificial_TUs.tsv
      gene input: example_data/regulonDB/artificial_genes.tsv
      operon input: example_data/regulonDB/artificial_operons.tsv
      output directory: results/regulonDB/
      promoter input: example_data/regulonDB/artificial_promoters.tsv
    UniProt:
      input file: example_data/UniProt/s_aureus_domains_shortened.txt
      output file: results/UniProt/domains.tsv
    VCF Merger:
      input directory: example_data/vcf_merger/
      output file: results/vcf_merger/mutation.tsv
Run:
  Default:
    clean up NGS output directory: true
    delete old analysis output: true
    open NGS output directory: true
    open analysis output directory: true
    open parser output directory: true
    run TFBS analysis: true
    run adjust operon promoters: true
    run coding region analysis: true
    run genes of interest analysis: true
    run protein domain analysis: true
    run regulation analysis: true
  User:
    clean up NGS output directory: true
    delete old analysis output: true
    open NGS output directory: true
    open analysis output directory: true
    open parser output directory: true
    run TFBS analysis: true
    run adjust operon promoters: true
    run coding region analysis: true
    run genes of interest analysis: true
    run protein domain analysis: true
    run regulation analysis: true
Windows:
  Default:
    Analysis:
      PWM number of sequence threshold: 5
      TF MSA path: example_data/mutation_analysis/artificial/TF_MSA.fasta
      TFBS path: example_data/mutation_analysis/artificial/TFBS.tsv
      TFBS random mutations: 15
      gene path: example_data/mutation_analysis/artificial/genes.tsv
      genes of interest (name long): genes of interest
      genes of interest (name short): GoI
      interest path: example_data/mutation_analysis/artificial/genes_of_interest.tsv
      mutation path: example_data/mutation_analysis/artificial/mutations.tsv
      other genes (name long): other genes
      other genes (name short): other
      output directory: results/mutation_analysis/
      protein domain path: example_data/mutation_analysis/artificial/domains.tsv
      regulation path: example_data/mutation_analysis/artificial/regulation.tsv
      relative promoter start: -100
      substitution matrix path: substitution_matrices/PAM10.tsv
    NGS:
      BWA executable: D:/Programs/bwa-0.7.12/bwa.EXE
      SAMTools executable: D:/Programs/samtools-1.3/samtools.EXE
      VarScan executable: D:/Programs/VarScan.v2.3.9/varscan.JAR
      output directory: results/NGS/
      p-value: 0.05
      quality control cut-off: 30
      reads directory: example_data/NGS/reads/
      reference genome path: example_data/NGS/ref_genome.fasta
    PATRIC:
      input file: example_data/PATRIC/resistance.csv
      output file: results/PATRIC/resistance.tsv
    RegulonDB:
      TF MSA input: example_data/regulonDB/artificial_TF_MSA.txt
      TF-TF input: example_data/regulonDB/artificial_TF_TF.tsv
      TF-TU input: example_data/regulonDB/artificial_TF_TU.tsv
      TF-gene input: example_data/regulonDB/artificial_TF_gene.tsv
      TF-operon input: example_data/regulonDB/artificial_TF_operon.tsv
      TFBS input: example_data/regulonDB/artificial_TFBS.tsv
      TU input: example_data/regulonDB/artificial_TUs.tsv
      gene input: example_data/regulonDB/artificial_genes.tsv
      operon input: example_data/regulonDB/artificial_operons.tsv
      output directory: results/regulonDB/
      promoter input: example_data/regulonDB/artificial_promoters.tsv
    UniProt:
      input file: example_data/UniProt/s_aureus_domains_shortened.txt
      output file: results/UniProt/domains.tsv
    VCF Merger:
      input directory: example_data/vcf_merger/
      output file: results/vcf_merger/mutation.tsv
  GUI:
    colours:
      description text: '#4F81BD'
      description title: '#4F81BD'
      section title: '#C0504D'
      sub-section title: '#76923D'
    fonts:
      check button:
      - Calibri
      - 12
      description text:
      - Calibri
      - 11
      description title:
      - Calibri
      - 16
      - bold
      entry field label:
      - Calibri
      - 12
      entry field text:
      - Calibri
      - 10
      file chooser button:
      - Calibri
      - 11
      run button:
      - Calibri
      - 12
      section title:
      - Calibri
      - 16
      - bold
      status line:
      - Calibri
      - 12
      sub-section title:
      - Calibri
      - 12
      - bold
    heights:
      description frame: 250
    styles:
      theme: vista
    widths:
      description frame: 400
      description text: 390
      file/directory chooser button: 3
      file/directory entry field: 30
      left settings button: 15
      number entry field: 15
      right settings button: 15
      run button: 20
      save/cancel button: 15
      separator line width: 1
      status box: 50
      status box border: 1
    x-margins:
      column: 20
      description text:
      - 0
      - 0
      description title:
      - 0
      - 0
      empty check button:
      - 10
      - 0
      entry field label:
      - 0
      - 10
      entry field text:
      - 0
      - 0
      file chooser button:
      - 0
      - 0
      left settings button:
      - 0
      - 0
      right settings button:
      - 0
      - 0
      run button:
      - 0
      - 0
      section title:
      - 0
      - 0
      separator:
      - 0
      - 0
      status box frame:
      - 0
      - 0
      subsection title:
      - 0
      - 0
      text check button:
      - 0
      - 0
      text separator:
      - 0
      - 0
      window left: 5
      window right: 10
    y-margins:
      column:
      - 0
      - 0
      description text:
      - 0
      - 0
      description title:
      - 15
      - 0
      empty check button:
      - 0
      - 0
      entry field label:
      - 0
      - 0
      entry field text:
      - 2
      - 2
      field name:
      - 0
      - 0
      file chooser button:
      - 0
      - 0
      left settings button:
      - 0
      - 0
      right settings button:
      - 0
      - 0
      run button:
      - 0
      - 0
      section title:
      - 15
      - 0
      separator:
      - 10
      - 10
      status box frame:
      - 0
      - 0
      subsection title:
      - 0
      - 0
      text check button:
      - 0
      - 0
      text separator:
      - 0
      - 0
      window bottom: 10
  User:
    Analysis:
      PWM number of sequence threshold: 5
      TF MSA path: example_data/mutation_analysis/artificial/TF_MSA.fasta
      TFBS path: example_data/mutation_analysis/artificial/TFBS.tsv
      TFBS random mutations: 15
      gene path: example_data/mutation_analysis/artificial/genes.tsv
      genes of interest (name long): genes of interest
      genes of interest (name short): GoI
      interest path: example_data/mutation_analysis/artificial/genes_of_interest.tsv
      mutation path: example_data/mutation_analysis/artificial/mutations.tsv
      other genes (name long): other genes
      other genes (name short): other
      output directory: results/mutation_analysis/
      protein domain path: example_data/mutation_analysis/artificial/domains.tsv
      regulation path: example_data/mutation_analysis/artificial/regulation.tsv
      relative promoter start: -100
      substitution matrix path: substitution_matrices/PAM10.tsv
    NGS:
      BWA executable: D:/Programs/bwa-0.7.12/bwa.EXE
      SAMTools executable: D:/Programs/samtools-1.3/samtools.EXE
      VarScan executable: D:/Programs/VarScan.v2.3.9/varscan.JAR
      output directory: results/NGS/
      p-value: 0.05
      quality control cut-off: 30
      reads directory: example_data/NGS/reads/
      reference genome path: example_data/NGS/ref_genome.fasta
    PATRIC:
      input file: example_data/PATRIC/resistance.csv
      output file: results/PATRIC/resistance.tsv
    RegulonDB:
      TF MSA input: example_data/regulonDB/artificial_TF_MSA.txt
      TF-TF input: example_data/regulonDB/artificial_TF_TF.tsv
      TF-TU input: example_data/regulonDB/artificial_TF_TU.tsv
      TF-gene input: example_data/regulonDB/artificial_TF_gene.tsv
      TF-operon input: example_data/regulonDB/artificial_TF_operon.tsv
      TFBS input: example_data/regulonDB/artificial_TFBS.tsv
      TU input: example_data/regulonDB/artificial_TUs.tsv
      gene input: example_data/regulonDB/artificial_genes.tsv
      operon input: example_data/regulonDB/artificial_operons.tsv
      output directory: results/regulonDB/
      promoter input: example_data/regulonDB/artificial_promoters.tsv
    UniProt:
      input file: example_data/UniProt/s_aureus_domains_shortened.txt
      output file: results/UniProt/domains.tsv
    VCF Merger:
      input directory: example_data/vcf_merger/
      output file: results/vcf_merger/mutation.tsv