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VEBER Philippe
codepi
Commits
02b0d86b
Commit
02b0d86b
authored
Oct 09, 2019
by
Carine Rey
Browse files
add option --dnds (calc dn ds dn/ds trees; add option --gt (calc gene trees)
parent
ca2ce705
Changes
5
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5 changed files
with
66 additions
and
12 deletions
+66
-12
app/reviewphiltrans_app.ml
app/reviewphiltrans_app.ml
+14
-5
lib/detection_pipeline.ml
lib/detection_pipeline.ml
+11
-0
lib/real_dataset.ml
lib/real_dataset.ml
+35
-6
lib/real_dataset.mli
lib/real_dataset.mli
+5
-0
lib/testnh.ml
lib/testnh.ml
+1
-1
No files found.
app/reviewphiltrans_app.ml
View file @
02b0d86b
...
...
@@ -16,6 +16,8 @@ let realdata_main ~use_diffsel
~
use_topological
~
use_identical
~
no_use_multinomial
~
calc_dnds
~
calc_gene_trees
~
indir
~
outdir
~
np
~
mem
()
=
let
loggers
=
[
Console_logger
.
create
()
;
...
...
@@ -37,9 +39,14 @@ let realdata_main ~use_diffsel
sw
use_multinomial
`Multinomial
;
]
in
let
pal
=
List
.
filter_opt
[
sw
calc_dnds
`DnDs
;
sw
calc_gene_trees
`GeneTree
;
]
in
List
.
concat
[
Repo
.
shift
"Merged_results"
(
Real_dataset
.
repo
meths
rd
)
;
Repo
.
shift
"PreParsed_Dataset"
(
Real_dataset
.
repo_parsed_rd
rd
);
Repo
.
shift
"PreParsed_Dataset"
(
Real_dataset
.
repo_parsed_rd
pal
rd
);
]
|>
Bistro_utils
.
Repo
.
build_main
~
outdir
~
loggers
?
np
?
mem
...
...
@@ -66,10 +73,10 @@ let realdata_command =
flag
"--identical"
no_arg
~
doc
:
" use the identical method (fast)."
and
no_use_multinomial
=
flag
"--no-multinomial"
no_arg
~
doc
:
" not use the multinomial method (very fast so by default)."
(* and preview
=
*
flag "--
preview-mode
" no_arg ~doc:"
Preview mode
"
*
and calc_
dnd
s =
*
flag "--
dnds
" no_arg ~doc:" calculate
dn ds dnds
trees (slow)."
*)
and
calc_dnds
=
flag
"--
dnds
"
no_arg
~
doc
:
"
calculate dn ds dnds trees (slow).
"
and
calc_
gene_tree
s
=
flag
"--
gt
"
no_arg
~
doc
:
" calculate
gene
trees (slow)."
and
np
=
flag
"--np"
(
optional
int
)
~
doc
:
"INT Number of available processors"
and
mem
=
...
...
@@ -82,6 +89,8 @@ let realdata_command =
~
use_topological
~
use_identical
~
no_use_multinomial
~
calc_dnds
~
calc_gene_trees
~
indir
~
outdir
~
np
~
mem
]
...
...
lib/detection_pipeline.ml
View file @
02b0d86b
...
...
@@ -17,6 +17,9 @@ module Make(D : Dataset) = struct
let
phylip_nucleotide_alignment
d
=
Bppsuite
.
fna2phy
~
fna
:
(
nucleotide_alignment
d
)
let
gene_tree
d
=
Tree_dataset
.
raxmlng_fna
~
fna
:
(
nucleotide_alignment
d
)
()
let
identical
d
=
let
tree_sc
=
Tree_dataset
.
prepare_sc_tree
(
tree
d
)
in
let
tree_id
=
Tree_dataset
.
prepare_tree_with_node_id
(
tree
d
)
in
...
...
@@ -90,4 +93,12 @@ module Make(D : Dataset) = struct
let
tree
=
tree
d
in
Pcoc
.
pcoc
~
catx_est
:
ncat
~
plot_complete
:
false
~
gamma
~
faa
~
tree
()
|>
Pcoc
.
results
let
dn_ds_dnds_trees
d
=
Testnh
.
dn_ds_trees_real_data
~
fna
:
(
nucleotide_alignment
d
)
~
tree
:
(
tree
d
)
()
let
dn_tree
d
=
(
dn_ds_dnds_trees
d
)
.
dn_tsv
let
ds_tree
d
=
(
dn_ds_dnds_trees
d
)
.
ds_tsv
let
dnds_tree
d
=
(
dn_ds_dnds_trees
d
)
.
dnds_tsv
end
lib/real_dataset.ml
View file @
02b0d86b
...
...
@@ -17,6 +17,10 @@ type meth =
`Identical
|
`Diffsel
]
type
pa
=
[
`DnDs
|
`GeneTree
]
module
Family
:
sig
type
dataset
=
t
type
t
...
...
@@ -92,6 +96,12 @@ let maybe_apply_method meths f m =
Some
(
implementation
f
m
)
else
None
let
maybe_apply_parralel_analyses
pal
p
=
if
List
.
mem
pal
p
~
equal
:
Poly
.
equal
then
true
else
false
let
result_table
meths
rd
=
let
families
=
families
rd
in
List
.
map
families
~
f
:
(
fun
f
->
...
...
@@ -113,13 +123,32 @@ let repo meths rd =
Bistro_utils
.
Repo
.
item
[
name
^
".tsv"
]
table
)
let
repo_parsed_rd
rd
=
let
repo_parsed_rd
pal
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
)
^
".species_tree.nhx"
]
(
Family
.
tree
f
);
Bistro_utils
.
Repo
.
item
[(
Family
.
name
f
)
^
".fna"
]
(
Family
.
nucleotide_alignment
f
);
Bistro_utils
.
Repo
.
item
[(
Family
.
name
f
)
^
".nw"
]
(
DP
.
gene_tree
f
);
]
|>
Repo
.
shift
(
Family
.
name
f
);
[
Bistro_utils
.
Repo
.
item
[(
Family
.
name
f
)
^
".faa"
]
(
DP
.
amino_acid_alignment
f
);
Bistro_utils
.
Repo
.
item
[(
Family
.
name
f
)
^
".species_tree.nhx"
]
(
Family
.
tree
f
);
Bistro_utils
.
Repo
.
item
[(
Family
.
name
f
)
^
".fna"
]
(
Family
.
nucleotide_alignment
f
);
];
if
(
maybe_apply_parralel_analyses
pal
`GeneTree
)
then
[
Bistro_utils
.
Repo
.
item
[(
Family
.
name
f
)
^
".nw"
]
(
DP
.
gene_tree
f
);
]
else
[]
;
if
(
maybe_apply_parralel_analyses
pal
`DnDs
)
then
[
[
Bistro_utils
.
Repo
.
item
[(
Family
.
name
f
)
^
".dn.tsv"
]
(
DP
.
dn_tree
f
);
Bistro_utils
.
Repo
.
item
[(
Family
.
name
f
)
^
".ds.tsv"
]
(
DP
.
ds_tree
f
);
Bistro_utils
.
Repo
.
item
[(
Family
.
name
f
)
^
".dnds.tsv"
]
(
DP
.
dnds_tree
f
);
]
|>
Repo
.
shift
"DnDs"
]
|>
List
.
concat
else
[]
;
]
|>
List
.
concat
|>
Repo
.
shift
(
Family
.
name
f
)
)
|>
List
.
concat
lib/real_dataset.mli
View file @
02b0d86b
...
...
@@ -13,6 +13,10 @@ type meth =
`Identical
|
`Diffsel
]
type
pa
=
[
`DnDs
|
`GeneTree
]
val
make
:
tree_path
:
string
->
alignment_dir_path
:
string
->
...
...
@@ -28,6 +32,7 @@ val repo :
t
->
Bistro_utils
.
Repo
.
t
val
repo_parsed_rd
:
pa
list
->
t
->
Bistro_utils
.
Repo
.
t
module
Family
:
sig
...
...
lib/testnh.ml
View file @
02b0d86b
...
...
@@ -236,7 +236,7 @@ let format_dn_ds ~ali_prefix ~(dn_tree:_ workflow) ~(ds_tree:_ workflow): direct
]
]
let
dn_ds_trees_real_data
~
ali_prefix
~
tree
~
fna
()
:
dnds_real
=
let
dn_ds_trees_real_data
?
(
ali_prefix
=
"gene"
)
~
tree
~
fna
()
:
dnds_real
=
let
run_bppml
=
bppml_mapnh
~
descr
:
(
"."
^
ali_prefix
)
~
tree
~
fna
in
let
dn_tree
=
Workflow
.
select
run_bppml
[
"mapping_counts_per_type_dN.dnd"
]
in
let
ds_tree
=
Workflow
.
select
run_bppml
[
"mapping_counts_per_type_dS.dnd"
]
in
...
...
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