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VEBER Philippe
codepi
Commits
1fa08ee7
Commit
1fa08ee7
authored
Nov 03, 2020
by
Philippe Veber
Browse files
Orthomam: tree output for the whole database
parent
2f0ee844
Changes
2
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2 changed files
with
20 additions
and
7 deletions
+20
-7
lib/orthomam.ml
lib/orthomam.ml
+14
-7
lib/orthomam.mli
lib/orthomam.mli
+6
-0
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lib/orthomam.ml
View file @
1fa08ee7
...
...
@@ -69,7 +69,7 @@ let%pworkflow clip_tree_on_alignment tree ali =
let
omm_tree_of_db
db
=
Workflow
.
input
(
Orthomam_db
.
tree
db
)
let
annotate_convergent_species_in_tree
(
tree
:
newick
file
)
species
:
n
ewick
file
=
let
annotate_convergent_species_in_tree
(
tree
:
newick
file
)
species
:
n
hx
file
=
Workflow
.
path_plugin
~
version
:
3
~
descr
:
"tree_of_convergent_species"
(
let
open
Phylogenetics
in
let
%
pdeps
species
=
species
...
...
@@ -359,14 +359,16 @@ module Q = struct
Workflow
.
input
(
q
.
alignment
:>
string
)
|>
remove_unobserved_sequences_from_alignment
let
omm_tree_with_branch_lengths
~
branch_length_unit
=
match
branch_length_unit
with
|
`Nucleotide
->
estimated_nucleotide_tree
|
`Amino_acid
->
estimated_amino_acid_tree
|
`Codon
->
estimated_codon_tree
let
tree
~
branch_length_unit
q
=
let
omm_tree_with_branch_lengths
=
match
branch_length_unit
with
|
`Nucleotide
->
estimated_nucleotide_tree
q
.
db
|
`Amino_acid
->
estimated_amino_acid_tree
q
.
db
|
`Codon
->
estimated_codon_tree
q
.
db
in
clip_tree_on_alignment
(
annotate_convergent_species_in_tree
omm_tree_with_branch_lengths
q
.
convergent_species
)
(
annotate_convergent_species_in_tree
(
omm_tree_with_branch_lengths
~
branch_length_unit
q
.
db
)
q
.
convergent_species
)
(
alignment
q
)
let
nucleotide_alignment
q
=
...
...
@@ -375,6 +377,11 @@ end
include
Q
let
tree_of_db
db
~
branch_length_unit
~
convergent_species
=
annotate_convergent_species_in_tree
(
omm_tree_with_branch_lengths
~
branch_length_unit
db
)
(
Workflow
.
data
convergent_species
)
include
Detection_pipeline
.
Make
(
Q
)
let
species_with_echolocation
=
[
...
...
lib/orthomam.mli
View file @
1fa08ee7
...
...
@@ -19,6 +19,12 @@ val alignment : query -> phylip file
val
nucleotide_alignment
:
query
->
nucleotide_fasta
file
val
tree_of_db
:
Orthomam_db
.
t
->
branch_length_unit
:
[
`Nucleotide
|
`Amino_acid
|
`Codon
]
->
convergent_species
:
string
list
->
nhx
file
val
tree
:
branch_length_unit
:
[
`Nucleotide
|
`Amino_acid
|
`Codon
]
->
query
->
...
...
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