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Adding example input files for the AHRD Trainer (Parameter Optimizati…

…on).
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asishallab committed Apr 7, 2016
1 parent fed2173 commit ebcf9556d9f0f4270b33d0ccc933f0c2db7db34e
Showing with 39 additions and 0 deletions.
  1. +38 −0 test/resources/trainer_example_input.yml
  2. +1 −0 trainer_example_input.yml
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proteins_fasta: ./test/resources/proteins.fasta
references_fasta: ./test/resources/references.fasta

blast_dbs:
swissprot:
weight: 653
description_score_bit_score_weight: 2.717061
file: ./test/resources/swissprot_blast8_tabular.txt
database: ./test/resources/swissprot_blast_db.fasta
blacklist: ./test/resources/blacklist_descline.txt
filter: ./test/resources/filter_descline_sprot.txt
token_blacklist: ./test/resources/blacklist_token.txt

trembl:
weight: 904
description_score_bit_score_weight: 2.590211
file: ./test/resources/trembl_blast8_tabular.txt
database: ./test/resources/trembl_blast_db.fasta
blacklist: ./test/resources/blacklist_descline.txt
filter: ./test/resources/filter_descline_trembl.txt
token_blacklist: ./test/resources/blacklist_token.txt

tair:
weight: 854
description_score_bit_score_weight: 2.917405
file: ./test/resources/tair_blast8_tabular.txt
database: ./test/resources/tair_blast_db.fasta
fasta_header_regex: "^>(?<accession>[aA][tT][0-9mMcC][gG]\\d+(\\.\\d+)?)\\s+\\|[^\\|]+\\|\\s+(?<description>[^\\|]+)(\\s*\\|.*)?$"
blacklist: ./test/resources/blacklist_descline.txt
filter: ./test/resources/filter_descline_tair.txt
token_blacklist: ./test/resources/blacklist_token.txt

token_score_bit_score_weight: 0.468
token_score_database_score_weight: 0.2098
token_score_overlap_score_weight: 0.3221
output: ./test/ahrd_output.csv
path_log: ./test/sim_anneal_path_log.csv
remember_simulated_annealing_path: true

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