Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in / Register
Toggle navigation
Open sidebar
VEBER Philippe
codepi
Commits
91b4df22
Commit
91b4df22
authored
Oct 08, 2019
by
Carine Rey
Browse files
realdata: add a output repo with parsed input files
parent
5719e39f
Changes
3
Hide whitespace changes
Inline
Side-by-side
Showing
3 changed files
with
20 additions
and
3 deletions
+20
-3
app/reviewphiltrans_app.ml
app/reviewphiltrans_app.ml
+6
-3
lib/real_dataset.ml
lib/real_dataset.ml
+11
-0
lib/real_dataset.mli
lib/real_dataset.mli
+3
-0
No files found.
app/reviewphiltrans_app.ml
View file @
91b4df22
...
...
@@ -37,7 +37,10 @@ let realdata_main ~use_diffsel
sw
use_multinomial
`Multinomial
;
]
in
Real_dataset
.
repo
meths
rd
List
.
concat
[
Repo
.
shift
"Merged_results"
(
Real_dataset
.
repo
meths
rd
)
;
Repo
.
shift
"PreParsed_Dataset"
(
Real_dataset
.
repo_parsed_rd
rd
);
]
|>
Bistro_utils
.
Repo
.
build_main
~
outdir
~
loggers
?
np
?
mem
let
realdata_command
=
...
...
@@ -54,9 +57,9 @@ let realdata_command =
and
use_pcoc
=
flag
"--pcoc"
no_arg
~
doc
:
" use the pcoc method (slow)."
and
use_pcoc_c60
=
flag
"--pcoc
_
c60"
no_arg
~
doc
:
" use the pcoc method with c60 profils (very_slow)."
flag
"--pcoc
-
c60"
no_arg
~
doc
:
" use the pcoc method with c60 profils (very_slow)."
and
use_pcoc_gamma
=
flag
"--pcoc
_
gamma"
no_arg
~
doc
:
" use the pcoc method with the gamma option (very_slow)."
flag
"--pcoc
-
gamma"
no_arg
~
doc
:
" use the pcoc method with the gamma option (very_slow)."
and
use_topological
=
flag
"--topological"
no_arg
~
doc
:
" use the topological method (fast)."
and
use_identical
=
...
...
lib/real_dataset.ml
View file @
91b4df22
open
Core_kernel
open
Bistro
open
Bistro_utils
type
t
=
{
tree_path
:
string
;
...
...
@@ -111,3 +112,13 @@ let repo meths rd =
List
.
map
(
result_table
meths
rd
)
~
f
:
(
fun
(
name
,
table
)
->
Bistro_utils
.
Repo
.
item
[
name
^
".tsv"
]
table
)
let
repo_parsed_rd
rd
=
let
families
=
families
rd
in
List
.
map
families
~
f
:
(
fun
f
->
[
Bistro_utils
.
Repo
.
item
[(
Family
.
name
f
)
^
".faa"
]
(
DP
.
amino_acid_alignment
f
);
Bistro_utils
.
Repo
.
item
[(
Family
.
name
f
)
^
".nhx"
]
(
Family
.
tree
f
);
Bistro_utils
.
Repo
.
item
[(
Family
.
name
f
)
^
".fna"
]
(
Family
.
nucleotide_alignment
f
);
]
|>
Repo
.
shift
(
Family
.
name
f
);
)
|>
List
.
concat
lib/real_dataset.mli
View file @
91b4df22
...
...
@@ -27,6 +27,9 @@ val repo :
meth
list
->
t
->
Bistro_utils
.
Repo
.
t
val
repo_parsed_rd
:
t
->
Bistro_utils
.
Repo
.
t
module
Family
:
sig
type
t
val
tree
:
t
->
nhx
pworkflow
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment