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bioinfo: added Busco
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@pveber
pveber committed Sep 26, 2019
1 parent 532ef7c commit 0f10c39
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168 changes: 168 additions & 0 deletions lib/bioinfo/bistro_bioinfo.ml
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Original file line number Diff line number Diff line change
Expand Up @@ -2875,3 +2875,171 @@ module Star = struct
]
|> sorted_mapped_reads
end

module Busco = struct
let img = [ docker_image ~account:"pveber" ~name:"busco" ~tag:"3.0.2" () ]

type db = [
| `bacteria
| `proteobacteria
| `rhizobiales
| `betaproteobacteria
| `gammaproteobacteria
| `enterobacteriales
| `deltaepsilonsub
| `actinobacteria
| `cyanobacteria
| `firmicutes
| `clostridia
| `lactobacillales
| `bacillales
| `bacteroidetes
| `spirochaetes
| `tenericutes
| `eukaryota
| `fungi
| `microsporidia
| `dikarya
| `ascomycota
| `pezizomycotina
| `eurotiomycetes
| `sordariomyceta
| `saccharomyceta
| `saccharomycetales
| `basidiomycota
| `metazoa
| `nematoda
| `arthropoda
| `insecta
| `endopterygota
| `hymenoptera
| `diptera
| `vertebrata
| `actinopterygii
| `tetrapoda
| `aves
| `mammalia
| `euarchontoglires
| `laurasiatheria
| `embryophyta
| `protists_ensembl
| `alveolata_stramenophiles_ensembl
]

let string_of_db = function
| `bacteria -> "bacteria"
| `proteobacteria -> "proteobacteria"
| `rhizobiales -> "rhizobiales"
| `betaproteobacteria -> "betaproteobacteria"
| `gammaproteobacteria -> "gammaproteobacteria"
| `enterobacteriales -> "enterobacteriales"
| `deltaepsilonsub -> "deltaepsilonsub"
| `actinobacteria -> "actinobacteria"
| `cyanobacteria -> "cyanobacteria"
| `firmicutes -> "firmicutes"
| `clostridia -> "clostridia"
| `lactobacillales -> "lactobacillales"
| `bacillales -> "bacillales"
| `bacteroidetes -> "bacteroidetes"
| `spirochaetes -> "spirochaetes"
| `tenericutes -> "tenericutes"
| `eukaryota -> "eukaryota"
| `fungi -> "fungi"
| `microsporidia -> "microsporidia"
| `dikarya -> "dikarya"
| `ascomycota -> "ascomycota"
| `pezizomycotina -> "pezizomycotina"
| `eurotiomycetes -> "eurotiomycetes"
| `sordariomyceta -> "sordariomyceta"
| `saccharomyceta -> "saccharomyceta"
| `saccharomycetales -> "saccharomycetales"
| `basidiomycota -> "basidiomycota"
| `metazoa -> "metazoa"
| `nematoda -> "nematoda"
| `arthropoda -> "arthropoda"
| `insecta -> "insecta"
| `endopterygota -> "endopterygota"
| `hymenoptera -> "hymenoptera"
| `diptera -> "diptera"
| `vertebrata -> "vertebrata"
| `actinopterygii -> "actinopterygii"
| `tetrapoda -> "tetrapoda"
| `aves -> "aves"
| `mammalia -> "mammalia"
| `euarchontoglires -> "euarchontoglires"
| `laurasiatheria -> "laurasiatheria"
| `embryophyta -> "embryophyta"
| `protists_ensembl -> "protists_ensembl"
| `alveolata_stramenophiles_ensembl -> "alveolata_stramenophiles_ensembl"

let file_of_db = function
| `protists_ensembl
| `alveolata_stramenophiles_ensembl as x ->
string_of_db x
| x -> string_of_db x ^ "_odb9"

let fetch_db (db : db) =
let url =
sprintf
"http://busco.ezlab.org/v2/datasets/%s.tar.gz"
(file_of_db db)
in
Bistro_unix.wget url
|> Bistro_unix.tar_xfz ~strip_components:1


let config_file = seq ~sep:"\n" [
string "[busco]" ;
seq ~sep:" " [ string "out_path =" ; dest ] ;
string {|
[tblastn]
path = /usr/bin/

[makeblastdb]
path = /usr/bin/

[augustus]
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin/

[etraining]
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin/

[gff2gbSmallDNA.pl]
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/scripts/
[new_species.pl]
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/scripts/
[optimize_augustus.pl]
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/scripts/

[hmmsearch]
path = /usr/local/bin/

[Rscript]
path = /usr/bin/
|}
]

let string_of_mode = function
| `genome -> "genome"
| `transcriptome -> "transcriptome"
| `proteins -> "proteins"

let busco ?evalue ?limit ?tarzip ~threads ~mode ~db fa =
Workflow.shell ~descr:"busco" ~np:threads [
within_container img (
and_list [
cmd "" [ seq ~sep:"" [ string "export BUSCO_CONFIG_FILE=" ; file_dump config_file ] ] ;
cmd "run_BUSCO.py" [
opt "--in" dep fa ;
opt "--lineage" dep (fetch_db db) ;
opt "--mode" (string_of_mode % string) mode ;
opt "--out" string "busco" ;
opt "--cpu" Fn.id np ;
option (opt "--evalue" float) evalue ;
option (opt "--limit" int) limit ;
option (flag string "--tarzip") tarzip ;
]
]
)
]
end
61 changes: 61 additions & 0 deletions lib/bioinfo/bistro_bioinfo.mli
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Original file line number Diff line number Diff line change
Expand Up @@ -1021,6 +1021,67 @@ module Quast : sig
[`quast] dworkflow
end

module Busco : sig
val img : Shell_dsl.container_image list

type db = [
| `bacteria
| `proteobacteria
| `rhizobiales
| `betaproteobacteria
| `gammaproteobacteria
| `enterobacteriales
| `deltaepsilonsub
| `actinobacteria
| `cyanobacteria
| `firmicutes
| `clostridia
| `lactobacillales
| `bacillales
| `bacteroidetes
| `spirochaetes
| `tenericutes
| `eukaryota
| `fungi
| `microsporidia
| `dikarya
| `ascomycota
| `pezizomycotina
| `eurotiomycetes
| `sordariomyceta
| `saccharomyceta
| `saccharomycetales
| `basidiomycota
| `metazoa
| `nematoda
| `arthropoda
| `insecta
| `endopterygota
| `hymenoptera
| `diptera
| `vertebrata
| `actinopterygii
| `tetrapoda
| `aves
| `mammalia
| `euarchontoglires
| `laurasiatheria
| `embryophyta
| `protists_ensembl
| `alveolata_stramenophiles_ensembl
]

val busco :
?evalue:float ->
?limit:int ->
?tarzip:bool ->
threads:int ->
mode:[`genome | `transcriptome | `proteins] ->
db:db ->
fasta pworkflow ->
directory pworkflow
end

(** {3 Differential analysis} *)

module DESeq2 : sig
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