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VEBER Philippe
codepi
Commits
927ad8f5
Commit
927ad8f5
authored
Jun 18, 2018
by
Carine Rey
Browse files
add a new workflow: fna2faa
parent
c0acc5c5
Changes
2
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2 changed files
with
25 additions
and
2 deletions
+25
-2
lib/bppsuite.ml
lib/bppsuite.ml
+21
-2
lib/bppsuite.mli
lib/bppsuite.mli
+4
-0
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lib/bppsuite.ml
View file @
927ad8f5
...
...
@@ -9,7 +9,7 @@ let env = docker_image ~account:"carinerey" ~name:"bppsuite:06182018" ()
let
assign
k
v
=
seq
~
sep
:
"="
[
string
k
;
v
]
let
conf_file
~
tree
~
nb_sites
=
let
conf_file
_bppseqgen
~
tree
~
nb_sites
=
seq
~
sep
:
"
\n
"
[
assign
"input.tree.file"
(
dep
tree
)
;
assign
"output.sequence.file"
dest
;
...
...
@@ -30,6 +30,25 @@ let conf_file ~tree ~nb_sites =
let
bppseqgen
~
nb_sites
~
tree
:
nucleotide_fasta
workflow
=
workflow
~
descr
:
"bppsuite.bppseqgen"
[
cmd
"bppseqgen"
~
env
[
assign
"param"
(
file_dump
(
conf_file
~
tree
~
nb_sites
))
;
assign
"param"
(
file_dump
(
conf_file_bppseqgen
~
tree
~
nb_sites
))
;
]
]
let
conf_file_bppseqman
~
fna
=
seq
~
sep
:
"
\n
"
[
assign
"input.sequence.file"
(
dep
fna
)
;
assign
"output.sequence.file"
dest
;
string
{
|
alphabet
=
Codon
(
letter
=
DNA
)
genetic_code
=
Standard
input
.
alignment
=
true
sequence
.
manip
=
Translate
|
}
]
let
fna2faa
~
(
fna
:
nucleotide_fasta
workflow
)
:
aminoacid_fasta
workflow
=
workflow
~
descr
:
"bppsuite.fna2faa"
[
cmd
"bppseqman"
~
env
[
assign
"param"
(
file_dump
(
conf_file_bppseqman
~
fna
))
;
]
]
lib/bppsuite.mli
View file @
927ad8f5
...
...
@@ -6,3 +6,7 @@ val bppseqgen :
nb_sites
:
int
->
tree
:
nhx
workflow
->
nucleotide_fasta
workflow
val
fna2faa
:
fna
:
nucleotide_fasta
workflow
->
aminoacid_fasta
workflow
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