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VEBER Philippe
codepi
Commits
dfbcc03f
Commit
dfbcc03f
authored
Jan 18, 2019
by
Philippe Veber
Browse files
Convergence_detection: introduced simpler utility to plot alignments
parent
8b0788de
Changes
4
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4 changed files
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37 additions
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+37
-0
lib/convergence_detection.ml
lib/convergence_detection.ml
+18
-0
lib/convergence_detection.mli
lib/convergence_detection.mli
+8
-0
lib/debug.ml
lib/debug.ml
+4
-0
lib/pipeline2.ml
lib/pipeline2.ml
+7
-0
No files found.
lib/convergence_detection.ml
View file @
dfbcc03f
...
...
@@ -147,3 +147,21 @@ let plot_merge_results ?t_choices ~plot_all_sites ~(res_by_tools:result list) ~t
]
in
Workflow
.
select
inner
[
"results.svg"
]
let
plot_convergent_sites
?
(
plot_all_sites
=
true
)
~
alignment
~
detection_results
~
tree
()
=
Workflow
.
shell
~
descr
:
"plot_convergent_sites.py"
[
within_container
Pcoc
.
img
(
and_list
[
mkdir_p
dest
;
cmd
"python"
[
Utils
.
script_dump
Scripts
.[
diffsel_script_utils
;
plot_data
;
plot_convergent_sites
]
;
opt
"-tsv"
dep
detection_results
;
opt
"-msa"
dep
alignment
;
opt
"-tree"
dep
tree
;
opt
"-out"
ident
(
dest
//
"plot.svg"
)
;
flag
string
"--all_sites"
plot_all_sites
;
]
]
)
]
|>
Fn
.
flip
Workflow
.
select
[
"plot.svg"
]
lib/convergence_detection.mli
View file @
dfbcc03f
...
...
@@ -41,3 +41,11 @@ val plot_merge_results :
tsv
:
text_file
pworkflow
->
unit
->
svg
pworkflow
val
plot_convergent_sites
:
?
plot_all_sites
:
bool
->
alignment
:
aminoacid_fasta
pworkflow
->
detection_results
:
text_file
pworkflow
->
tree
:
nhx
pworkflow
->
unit
->
svg
pworkflow
lib/debug.ml
View file @
dfbcc03f
...
...
@@ -25,6 +25,10 @@ let less w =
Sys
.
command
(
sprintf
"less %s"
(
path
w
))
|>
ignore
let
firefox
w
=
Sys
.
command
(
sprintf
"firefox %s"
(
path
w
))
|>
ignore
let
workflow_of_template
t
=
let
open
Bistro
.
Shell_dsl
in
Workflow
.
shell
[
...
...
lib/pipeline2.ml
View file @
dfbcc03f
...
...
@@ -104,3 +104,10 @@ let diffseldsparse d =
~
w_every
:
1
~
n_cycles
:
50
()
let
alignment_plot
d
=
Convergence_detection
.
plot_convergent_sites
~
tree
:
(
tree
d
)
~
alignment
:
(
amino_acid_alignment
d
)
~
detection_results
:
(
multinomial
d
)
()
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