Commit 0c1575dd authored by LANORE Vincent's avatar LANORE Vincent
Browse files

Removed command.py that was not supposed to be there

parent 5aebfca7
......@@ -54,7 +54,6 @@ test_val:
# -----------------------------------------------------------------------
# experiments on real data (only Besnard)
# -----------------------------------------------------------------------
.PHONY: fast_real
fast_real:
cd example && \
......@@ -72,40 +71,11 @@ real:
# -----------------------------------------------------------------------
# experiments on threshold choices
# -----------------------------------------------------------------------
.PHONY: analyses_seuils
analyses_seuils:
cd example && \
reviewphiltrans validation --outdir outdir_analyses_seuils --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 16 --no-ne --no-hapc --ns 1000 && \
mv dag.dot daganalyses_seuils.dot
.PHONY: analyses_everything_fast
analyses_everything_fast:
cd example && \
reviewphiltrans validation --outdir outdir_analyses_everything_fast --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 16 --ns 100 --fast && \
mv dag.dot daganalyses_everything_fast.dot
.PHONY: analyses_everything
analyses_everything:
cd example && \
reviewphiltrans validation --outdir outdir_analyses_everything --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 16 --ns 100 && \
mv dag.dot daganalyses_everything.dot
# -----------------------------------------------------------------------
# experiments on Ne values choices
# -----------------------------------------------------------------------
.PHONY: analyses_30Bloom_ne
analyses_30Bloom_ne:
cd example && \
reviewphiltrans validation --outdir outdir_analyses_tiragesBloomK30_ne --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4 --ns 500 --only-sim && \
mv dag.dot daganalyses_tiragesBloomK30_ne.dot
.PHONY: analyses_263Bloom_ne
analyses_263Bloom_ne:
.PHONY: analyses_we
analyses_we:
cd example && \
reviewphiltrans validation --outdir outdir_analyses_263SelectedProfiles_ne --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 4 --ns 500 --only-sim && \
mv dag.dot daganalyses_263SelectedProfiles_ne.dot
reviewphiltrans validation --outdir outdir_analyses_we --tree-dir trees_analyses_weekend --profile-fn aa_fitness/263SelectedProfiles.tsv --np 28 --ns 1000 && \
mv dag.dot daganalyses_we.dot
# -----------------------------------------------------------------------
# Cleaning and formatting
......
from ete3 import Tree
f_l=["./ensembl_3tr.nhx", "./cyp_coding.nhx"]
def m_bl(t_n, m):
t=Tree(t_n)
for n in t.traverse():
n.dist = n.dist * m
out_n = t_n.replace(".nhx",".bl_%i.nhx" %(m))
t.write(format=1, features=["Condition","Transition"], outfile = out_n)
list(map(lambda p: m_bl(p, 5), f_l))
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