Docker-in-Docker (DinD) capabilities of public runners deactivated. More info

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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