Module: ViralSeq::TcsDr

Defined in:

lib/viral_seq/tcs_dr.rb

Overview

store preset params for the DR pipeline. Used in the ‘tcs` command. run `tcs –dr_params [VERSION]` to pull the params json string for each version of DR.

Constant Summary

PARAMS =

{
  "v1" => {:platform_error_rate=>0.01,
  :primer_pairs=>
   [{:region=>"RT",
     :cdna=>
      "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCACTATAGGCTGTACTGTCCATTTATC",
     :forward=>
      "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGGCCATTGACAGAAGAAAAAATAAAAGC",
     :majority=>0,
     :end_join=>true,
     :end_join_option=>1,
     :overlap=>0,
     :TCS_QC=>true,
     :ref_genome=>"HXB2",
     :ref_start=>2648,
     :ref_end=>3257,
     :indel=>true,
     :trim=>false},
    {:region=>"PR",
     :cdna=>
      "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNCAGTTTAACTTTTGGGCCATCCATTCC",
     :forward=>
      "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTCAGAGCAGACCAGAGCCAACAGCCCCA",
     :majority=>0,
     :end_join=>true,
     :end_join_option=>3,
     :TCS_QC=>true,
     :ref_genome=>"HXB2",
     :ref_start=>0,
     :ref_end=>2591,
     :indel=>true,
     :trim=>true,
     :trim_ref=>"HXB2",
     :trim_ref_start=>2253,
     :trim_ref_end=>2549},
    {:region=>"IN",
     :cdna=>
      "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNATCGAATACTGCCATTTGTACTGC",
     :forward=>"GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNAAAAGGAGAAGCCATGCATG",
     :majority=>0,
     :end_join=>true,
     :end_join_option=>2,
     :overlap=>171,
     :TCS_QC=>true,
     :ref_genome=>"HXB2",
     :ref_start=>4384,
     :ref_end=>4751,
     :indel=>false,
     :trim=>false},
    {:region=>"V1V3",
     :cdna=>
      "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCCATTTTGCTYTAYTRABVTTACAATRTGC",
     :forward=>
      "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTTATGGGATCAAAGCCTAAAGCCATGTGTA",
     :majority=>0,
     :end_join=>true,
     :end_join_option=>1,
     :overlap=>0,
     :TCS_QC=>true,
     :ref_genome=>"HXB2",
     :ref_start=>6585,
     :ref_end=>7205..7210,
     :indel=>true,
     :trim=>false},
     {:region=>"CA",
      :cdna=>
       "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCAACAAGGTTTCTGTCATCCAATTTTTTAC",
      :forward=>
       "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGTCAGCCAAAATTACCCTATAGTGC",
      :majority=>0,
      :end_join=>true,
      :end_join_option=>1,
      :overlap=>0,
      :TCS_QC=>true,
      :ref_genome=>"HXB2",
      :ref_start=>1196,
      :ref_end=>1725,
      :indel=>true,
      :trim=>false}
     ]
  },

  "v2" => {:platform_error_rate=>0.01,
  :primer_pairs=>
  [{:region=>"RT",
    :cdna=>
      "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCACTATAGGCTGTACTGTCCATTTATC",
    :forward=>
      "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGGCCATTGACAGAAGAAAAAATAAAAGC",
    :majority=>0,
    :end_join=>true,
    :end_join_option=>1,
    :overlap=>0,
    :TCS_QC=>true,
    :ref_genome=>"HXB2",
    :ref_start=>2648,
    :ref_end=>3257,
    :indel=>true,
    :trim=>false},
    {:region=>"PR",
    :cdna=>
      "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNTTAACCTTTGGGCCATCCATTCC",
    :forward=>
      "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTCAGAGCAGACCAGAGCCAACAGCCCCA",
    :majority=>0,
    :end_join=>true,
    :end_join_option=>3,
    :TCS_QC=>true,
    :ref_genome=>"HXB2",
    :ref_start=>0,
    :ref_end=>2591,
    :indel=>true,
    :trim=>true,
    :trim_ref=>"HXB2",
    :trim_ref_start=>2253,
    :trim_ref_end=>2549},
    {:region=>"IN",
    :cdna=>
      "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNATCGAATACTGCCATTTGTACTGC",
    :forward=>"GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNAAAAGGAGAAGCCATGCATG",
    :majority=>0,
    :end_join=>true,
    :end_join_option=>2,
    :overlap=>171,
    :TCS_QC=>true,
    :ref_genome=>"HXB2",
    :ref_start=>4384,
    :ref_end=>4751,
    :indel=>false,
    :trim=>false},
    {:region=>"V1V3",
    :cdna=>
      "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCCATTTTGCTYTAYTRABVTTACAATRTGC",
    :forward=>
      "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTTATGGGATCAAAGCCTAAAGCCATGTGTA",
    :majority=>0,
    :end_join=>true,
    :end_join_option=>1,
    :overlap=>0,
    :TCS_QC=>true,
    :ref_genome=>"HXB2",
    :ref_start=>6585,
    :ref_end=>7205..7210,
    :indel=>true,
    :trim=>false},
    {:region=>"CA",
      :cdna=>
      "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCAACAAGGTTTCTGTCATCCAATTTTTTAC",
      :forward=>
      "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGTCAGCCAAAATTACCCTATAGTGC",
      :majority=>0,
      :end_join=>true,
      :end_join_option=>1,
      :overlap=>0,
      :TCS_QC=>true,
      :ref_genome=>"HXB2",
      :ref_start=>1196,
      :ref_end=>1725,
      :indel=>true,
      :trim=>false}
    ]
  },

  "v3" => {:platform_error_rate=>0.01,
  :primer_pairs=>
  [{:region=>"RT",
    :cdna=>
      "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTAAGGAATGGAGGTTCTTTCTGATG",
    :forward=>
      "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGGCCATTGACAGAAGAAAAAATAAAAGC",
    :majority=>0,
    :end_join=>true,
    :end_join_option=>1,
    :overlap=>0,
    :TCS_QC=>true,
    :ref_genome=>"HXB2",
    :ref_start=>2648,
    :ref_end=>3209,
    :indel=>true,
    :trim=>false},
    {:region=>"PR",
    :cdna=>
      "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNTTAACCTTTGGGCCATCCATTCC",
    :forward=>
      "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTCAGAGCAGACCAGAGCCAACAGCCCCA",
    :majority=>0,
    :end_join=>true,
    :end_join_option=>3,
    :TCS_QC=>true,
    :ref_genome=>"HXB2",
    :ref_start=>0,
    :ref_end=>2591,
    :indel=>true,
    :trim=>true,
    :trim_ref=>"HXB2",
    :trim_ref_start=>2253,
    :trim_ref_end=>2549},
    {:region=>"IN",
    :cdna=>
      "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCACAATCAKCACCTGCCATCTG",
    :forward=>"GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGCAGAAGTTATYCCAGCAGAAACA",
    :majority=>0,
    :end_join=>true,
    :end_join_option=>3,
    :TCS_QC=>true,
    :ref_genome=>"HXB2",
    :ref_start=>4509,
    :ref_end=>5048,
    :indel=>true,
    :trim=>false},
    {:region=>"V1V3",
    :cdna=>
      "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCCATTTTGCTYTAYTRABVTTACAATRTGC",
    :forward=>
      "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNTTATGGGATCAAAGCCTAAAGCCATGTGTA",
    :majority=>0,
    :end_join=>true,
    :end_join_option=>1,
    :overlap=>0,
    :TCS_QC=>true,
    :ref_genome=>"HXB2",
    :ref_start=>6585,
    :ref_end=>7205..7210,
    :indel=>true,
    :trim=>false},
    {:region=>"CA",
      :cdna=>
      "GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNCAGTCAACAAGGTTTCTGTCATCCAATTTTTTAC",
      :forward=>
      "GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAGNNNNGTCAGCCAAAATTACCCTATAGTGC",
      :majority=>0,
      :end_join=>true,
      :end_join_option=>1,
      :overlap=>0,
      :TCS_QC=>true,
      :ref_genome=>"HXB2",
      :ref_start=>1196,
      :ref_end=>1725,
      :indel=>true,
      :trim=>false}
    ]
  },


}