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VEBER Philippe
codepi
Commits
88297304
Commit
88297304
authored
Jan 15, 2021
by
Louis Duchemin
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Orthomam : adjusting pipeline upstream of rer_converge
parent
4a7cbafd
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88297304
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@@ -602,17 +602,24 @@ let rer_converge ?max_read ?transform ?weighted ?scale ?continuous ~db
let
open
Bistro_bio
in
let
module
RER
=
Rer_converge
in
let
species_tree
=
estimated_codon_tree
db
in
let
model
=
Iqtree
.
model_spec
~
freq_type
:
`F
`ECMK07
in
let
queries
=
alignments_of_db
db
|>
List
.
map
~
f
:
(
query
~
convergent_species
:
phenotypes
)
|>
Fn
.
flip
List
.
take
10
in
let
gene_ids
=
List
.
map
~
f
:
family_id
queries
in
let
ali_files
=
List
.
map
~
f
:
Q
.
alignment
queries
in
(* let model = Iqtree.model_spec ~freq_type:`F `ECMK07 in *)
let
gene_trees
=
List
.
map
~
f
:
(
fun
q
->
Iqtree
.
iqtree
~
te
:
species_tree
~
m
:
model
~
st
:
(
`CODON
1
)
(
`phylip
q
)
let
spp
=
iqtree_nexus_partition_file_of_alignment
q
in
let
clipped_tree
=
clip_tree_on_alignment
species_tree
q
in
Iqtree
.
iqtree
~
te
:
clipped_tree
(*~m:model*)
~
st
:
`DNA
~
spp
(
`phylip
q
)
|>
Iqtree
.
treefile
)
ali_files
|>
List
.
zip_exn
gene_ids
in
let
gene_tree_set
=
RER
.
gene_tree_file
gene_trees
in
let
phenotype
=
RER
.
phenotypes_of_convergent_species
phenotypes
in
...
...
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