Commit 60b0a78b authored by LANORE Vincent's avatar LANORE Vincent
Browse files

Added orthomam trees sims to init + added script/integration in init to count...

Added orthomam trees sims to init + added script/integration in init to count detections above threshold
parent 2dc1c773
......@@ -13,6 +13,10 @@ let auc ?mode d =
let gc_contents ?thirdpos:(tp=false) d =
d |> nucleotide_alignment |> Dbg.path |> Alistats.nucleotide_fasta_gc ~thirdpos:tp
let count_py w =
Sys.command (Core.sprintf "python lib/scripts/count_detected.py %s" (Dbg.path w))
|> ignore
let h0 =
bppseqgen_simulation
~hyp:Convergence_hypothesis.(H0 (Fixed 5.))
......@@ -59,6 +63,16 @@ let convdet_amaranth =
~tree:(`NHX "example/trees_analyses/C4AmaranthaceaePolyroot.nhx")
~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
let convdet_orthomam_aridity =
convdet_simulation
~tree:(`NHX "example/trees_analyses/orthomam_aridity.nhx")
~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
let convdet_orthomam_handpicked =
convdet_simulation
~tree:(`NHX "example/trees_analyses/orthomam_handpicked.nhx")
~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
let convdet_pairs ~bl n =
convdet_simulation
~tree:(`Pair_tree (bl /. 10., bl, n))
......
"""Usage:
count_detected.py <alignment>
"""
import pandas as pd
from docopt import docopt
arguments = docopt(__doc__, version='Naval Fate 2.0')
path = arguments["<alignment>"]
d = pd.read_csv(path, sep="\t")
mm = {"Topological_LG08":0.8, "PCOC":0.8, 'Tdg09_prob_post':0.99, 'Mutinomial_1MinusLRT':0.99}
for (k,v) in mm.items():
print(k, ":", (d[k] > v).sum())
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