# tRNAscan-SE 2.0 
# Configuration File

# default paths
bin_dir: /Users/runner/bioconda/conda-bld/trnascan-se_1642199529095/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin
lib_dir: /Users/runner/bioconda/conda-bld/trnascan-se_1642199529095/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/tRNAscan-SE
infernal_dir: {bin_dir}

# temporary files
temp_dir: /tmp
tmp_raw: {temp_dir}/tscan$$.raw
tmp_fa: {temp_dir}/tscan$$.fa
tmp_trnaseq_file: {temp_dir}/tscan$$.trna
tmp_masked_fa: {temp_dir}/tscan$$.masked.fa

# sequence process
really_big_number: 1000000000
upstream_len: 70
downstream_len: 70

# default search mode
cm_mode: infernal
# default cutoff bit score for infernal running as first pass scanner
infernal_fp_cutoff: 10
# default cutoff score for reporting of tRNA
cm_cutoff: 20
# default cutoff score for reporting of tRNA in organelles
organelle_cm_cutoff: 15
isotype_cm_cutoff.euk: 20
isotype_cm_cutoff.arch: 20
isotype_cm_cutoff.bact: 20
isotype_cm_cutoff.mito_mammal: 20
isotype_cm_cutoff.mito_vert: 20

# max size of -w parameter passed to covels when using a pre-scanner (eufind or tRNAscan)
max_tRNA_length: 500
# max size of -w param if only Cove is being used (too slow otherwise)	
max_cove_tRNA_length: 250
# max size of -w param if only cmsearch is being used 
max_cmsearch_tRNA_length: 250
# min length for average tRNA with no intron
min_tRNA_no_intron: 70
# min size of introns detected by parsing of coves output
min_intron_length: 3
# Below this score, tRNAs are checked for min primary and secondary structure
# scores to catch pseudogene repeats like rat ID & rodent B2 elements
min_cove_pseudo_filter_score: 55
# Below this score, tRNAs are checked for min primary and secondary structure
# scores to catch pseudogene repeats like rat ID & rodent B2 elements
min_cmsearch_pseudo_filter_score: 55
# Below this secondary structure score, tRNA is considered a pseudogene
min_ss_score: 5
# Below this primary structure score, tRNA is considered a pseudogene
min_hmm_score: 10

# legacy mode default searching parameters
# Intermediate score cutoff for use with eufindtRNA
eufind.intscore: -32.10
eufind.orig_intscore: -31.25    
eufind.bact_intscore: -36.0
eufind.arch_intscore: -36.0
eufind.strict_param: -s
# relaxed params to be used with eufindtRNA program by default
eufind.relaxed_param: -r
tscan.strict_param: -s
tscan.relaxed_param: -r
tscan.alt_param: -a

# default cutoff score for rescanning non-canonical introns
nci_scan_cutoff: 70
# default score for considering non-canonical intron
BHB_cm_cutoff: 6.5
# default cutoff score for rescanning split tRNA
split_tRNA_scan_cutoff: 38
# default cutoff score for half tRNA
half_tRNA_cutoff: 15
left_splicing_len: 27			 
right_splicing_len: 28			 

# alternate genetic code
gc_yeast_mito: {lib_dir}/gcode/gcode.ystmito
gc_vert_mito: {lib_dir}/gcode/gcode.vertmito
gc_invert_mito: {lib_dir}/gcode/gcode.invmito
gc_ciliate_cyto: {lib_dir}/gcode/gcode.cilnuc
gc_echinoderm_mito: {lib_dir}/gcode/gcode.echdmito
gc_other_mito: {lib_dir}/gcode/gcode.othmito
gc_marsu_mito: {lib_dir}/gcode/gcode.marsumito

# Infernal 1.1 covariance models
cm_dir: {lib_dir}/models
cm.general: {cm_dir}/TRNAinf.cm
cm.general-ns: {cm_dir}/TRNAinf-ns.cm
cm.general1415: {cm_dir}/TRNAinf-1415.cm
cm.general1415-ns: {cm_dir}/TRNAinf-1415-ns.cm
cm.eukaryota: {cm_dir}/TRNAinf-euk.cm
cm.eukaryota-ns: {cm_dir}/TRNAinf-euk-ns.cm
cm.archaea: {cm_dir}/TRNAinf-arch.cm
cm.archaea-ns: {cm_dir}/TRNAinf-arch-ns.cm
cm.bacteria: {cm_dir}/TRNAinf-bact.cm
cm.bacteria-ns: {cm_dir}/TRNAinf-bact-ns.cm
cm.arch_5h: {cm_dir}/TRNAinf-arch-5h.cm
cm.arch_3h: {cm_dir}/TRNAinf-arch-3h.cm

# COVE covariance models
cove_cm_dir: {lib_dir}/models
cove_cm.general: {cove_cm_dir}/TRNA2.cm
cove_cm.general-ns: {cove_cm_dir}/TRNA2ns.cm
cove_cm.eukaryota: {cove_cm_dir}/TRNA2-euk.cm
cove_cm.eukaryota-ns: {cove_cm_dir}/TRNA2-eukns.cm
cove_cm.archaea: {cove_cm_dir}/TRNA2-arch.cm
cove_cm.archaea-ns: {cove_cm_dir}/TRNA2-archns.cm
cove_cm.bacteria: {cove_cm_dir}/TRNA2-bact.cm
cove_cm.bacteria-ns: {cove_cm_dir}/TRNA2-bactns.cm
cove_cm.ESELC: {cove_cm_dir}/ESELC.cm
cove_cm.PSELC: {cove_cm_dir}/PSELC.cm

# Isotype-specific model db
isotype_cm_dir: {lib_dir}/models
isotype_cm.eukaryota: {isotype_cm_dir}/TRNAinf-euk-iso
isotype_cm.bacteria: {isotype_cm_dir}/TRNAinf-bact-iso
isotype_cm.archaea: {isotype_cm_dir}/TRNAinf-arch-iso

# tRNA-SeC models
euk_cm.SeC: {isotype_cm_dir}/TRNAinf-euk-SeC.cm
bact_cm.SeC: {isotype_cm_dir}/TRNAinf-bact-SeC.cm
arch_cm.SeC: {isotype_cm_dir}/TRNAinf-arch-SeC.cm

# Non-canonical intron models
nci_cm.cren: {cm_dir}/Cren-eury-BHB-noncan.cm
nci_cm.thaum: {cm_dir}/Thaum-BHB-noncan.cm

# Mito-tRNA model db
mito_cm_db_dir: {lib_dir}/models
mito_cm.mammal: {mito_cm_db_dir}/TRNAinf-mito-mammal
mito_cm.vert: {mito_cm_db_dir}/TRNAinf-mito-vert

# Mammalian mito-tRNA models
mito_cm_mammal_dir: {lib_dir}/models
mito_cm_mammal.Ala: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Ala.cm
mito_cm_mammal.Arg: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Arg.cm
mito_cm_mammal.Asn: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Asn.cm
mito_cm_mammal.Asp: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Asp.cm
mito_cm_mammal.Cys: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Cys.cm
mito_cm_mammal.Gln: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Gln.cm
mito_cm_mammal.Glu: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Glu.cm
mito_cm_mammal.Gly: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Gly.cm
mito_cm_mammal.His: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-His.cm
mito_cm_mammal.Ile: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Ile.cm
mito_cm_mammal.LeuTAA: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-LeuTAA.cm
mito_cm_mammal.LeuTAG: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-LeuTAG.cm
mito_cm_mammal.Lys: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Lys.cm
mito_cm_mammal.Met: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Met.cm
mito_cm_mammal.Phe: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Phe.cm
mito_cm_mammal.Pro: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Pro.cm
mito_cm_mammal.SerGCT: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-SerGCT.cm
mito_cm_mammal.SerTGA: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-SerTGA.cm
mito_cm_mammal.Thr: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Thr.cm
mito_cm_mammal.Trp: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Trp.cm
mito_cm_mammal.Tyr: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Tyr.cm
mito_cm_mammal.Val: {mito_cm_mammal_dir}/TRNAinf-mito-mammal-Val.cm

# Vertebrate mito-tRNA models
mito_cm_vert_dir: {lib_dir}/models
mito_cm_vert.Ala: {mito_cm_vert_dir}/TRNAinf-mito-vert-Ala.cm
mito_cm_vert.Arg: {mito_cm_vert_dir}/TRNAinf-mito-vert-Arg.cm
mito_cm_vert.Asn: {mito_cm_vert_dir}/TRNAinf-mito-vert-Asn.cm
mito_cm_vert.Asp: {mito_cm_vert_dir}/TRNAinf-mito-vert-Asp.cm
mito_cm_vert.Cys: {mito_cm_vert_dir}/TRNAinf-mito-vert-Cys.cm
mito_cm_vert.Gln: {mito_cm_vert_dir}/TRNAinf-mito-vert-Gln.cm
mito_cm_vert.Glu: {mito_cm_vert_dir}/TRNAinf-mito-vert-Glu.cm
mito_cm_vert.Gly: {mito_cm_vert_dir}/TRNAinf-mito-vert-Gly.cm
mito_cm_vert.His: {mito_cm_vert_dir}/TRNAinf-mito-vert-His.cm
mito_cm_vert.Ile: {mito_cm_vert_dir}/TRNAinf-mito-vert-Ile.cm
mito_cm_vert.LeuTAA: {mito_cm_vert_dir}/TRNAinf-mito-vert-LeuTAA.cm
mito_cm_vert.LeuTAG: {mito_cm_vert_dir}/TRNAinf-mito-vert-LeuTAG.cm
mito_cm_vert.Lys: {mito_cm_vert_dir}/TRNAinf-mito-vert-Lys.cm
mito_cm_vert.Met: {mito_cm_vert_dir}/TRNAinf-mito-vert-Met.cm
mito_cm_vert.Phe: {mito_cm_vert_dir}/TRNAinf-mito-vert-Phe.cm
mito_cm_vert.Pro: {mito_cm_vert_dir}/TRNAinf-mito-vert-Pro.cm
mito_cm_vert.SerGCT: {mito_cm_vert_dir}/TRNAinf-mito-vert-SerGCT.cm
mito_cm_vert.SerTGA: {mito_cm_vert_dir}/TRNAinf-mito-vert-SerTGA.cm
mito_cm_vert.Thr: {mito_cm_vert_dir}/TRNAinf-mito-vert-Thr.cm
mito_cm_vert.Trp: {mito_cm_vert_dir}/TRNAinf-mito-vert-Trp.cm
mito_cm_vert.Tyr: {mito_cm_vert_dir}/TRNAinf-mito-vert-Tyr.cm
mito_cm_vert.Val: {mito_cm_vert_dir}/TRNAinf-mito-vert-Val.cm

# to be used for sprinzl position alignment
# sprinzl_cm_dir: {lib_dir}/models
# sprinzl_cm.euk: {sprinzl_cm_dir}/euk_sprinzl.cm
# sprinzl_cm.arch: {sprinzl_cm_dir}/arch_sprinzl.cm
# sprinzl_cm.bact: {sprinzl_cm_dir}/bact_sprinzl.cm

# alternate covariance models
# To be used in place of default models
# Example:
# alt_cm_dir: /tmp
# alt_cm.Ala: {alt_cm_dir}/Ala.cm
# alt_cm.Arg: {alt_cm_dir}/Arg.cm
