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config.yml

!Docker/nested/config.yml

LTR_Finder/

build/

nested.egg-info/

# this version is just copied from a different branch, probably won't work as is

ltr:

  path: '/LTR_Finder/source/ltr_finder'

  prosite_path: &prosite_path /nested/dbs/prosite

  tRNAdb_path: &tRNAdb_path /LTR_Finder/source/tRNA/Athal-tRNAs.fa

  args:

    l: 32

    S: 3

    M: 0.2

    o: 2

    p: 15

    g: 80

    G: 5

    T: 2

    w: 2 #don't change, parsing format required!

    a: *prosite_path

    s: *tRNAdb_path

ltr_harvest:

  path: 'gt'

  command: 'ltrharvest'

  args:

    similar: 40

    maxlenltr: 3000

    maxdistltr: 20000

    mintsd: 4

    maxtsd: 10

miteFinder:

  path: '/miteFinder_repository/bin/miteFinder_linux_x64'

  args:

    pattern_scoring: '/miteFinder_repository/profile/pattern_scoring.txt'

    threshold: 0.5 

gt:

  path: 'gt'

  command: 'sketch'

  style_path: &style_path /nested/nested/config/gt.style

  args: 

    width: 1400

    style: *style_path

blastx:

  db_path: &db_path /nested/dbs/gydb_arh_chdcr/gydb_arh_chdcr.fa

  args:

    db: *db_path

    outfmt: 5 #don't change, parsing format required!

    num_threads: 3

    dbsize: 90000

    word_size: 2

    evalue: 1

tool_order:

  trf: 1

  tidecluster: 2

  mite: 10

  nester: 20

  solo_ltrs: 30

gff_format:

  sequence_ontology:

    te_base: nested_repeat

    domain: polypeptide_conserved_region

    te: repeat_fragment

    pbs: primer_binding_site

    ppt: RR_tract

    ltr: long_terminal_repeat

    tsr: target_site_duplication

igv_colors:

  nested_nester:

    default: '#a9a9a9'

    tsr_left: '#333333'

    tsr_right: '#333333'

    ltr_left: '#f032e6'

    ltr_right: '#f032e6'

    pbs: '#c7e9c0'

    ppt: '#41ab5d'

    GAG: '#225ea8'

    PROT: '#ffeda0'

    RT: '#feb24c'

    RH: '#fc4e2a'

    aRH: '#fc4e2a'

    INT: '#b10026'

    CHR: '#6a51a3'

  trf:

    tandem_repeat: '#33f5e8'

  mite:

    mite: '#025fc2'

    tir_left: '#04d442'

    tir_right: '#04d442'

  solo_ltrs:

    solo_ltr: '#7104c9'

logdir: /tmp/nested/logs