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VEBER Philippe
codepi
Commits
0c1575dd
Commit
0c1575dd
authored
Jul 20, 2018
by
LANORE Vincent
Browse files
Removed command.py that was not supposed to be there
parent
5aebfca7
Changes
2
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2 changed files
with
4 additions
and
47 deletions
+4
-47
Makefile
Makefile
+4
-34
example/trees_analyses_weekend/command.py
example/trees_analyses_weekend/command.py
+0
-13
No files found.
Makefile
View file @
0c1575dd
...
...
@@ -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_n
e
--tree-dir
trees
4
analyses
--profile-fn
aa_fitness/263SelectedProfiles.tsv
--np
4
--ns
500
--only-sim
&&
\
mv
dag.dot daganalyses_
263SelectedProfiles_n
e.dot
reviewphiltrans validation
--outdir
outdir_analyses_
w
e
--tree-dir
trees
_
analyses
_weekend
--profile-fn
aa_fitness/263SelectedProfiles.tsv
--np
28
--ns
1000
&&
\
mv
dag.dot daganalyses_
w
e.dot
# -----------------------------------------------------------------------
# Cleaning and formatting
...
...
example/trees_analyses_weekend/command.py
deleted
100644 → 0
View file @
5aebfca7
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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