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Add blast.ml to lib/bioinfo #38

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Add blast.ml to lib/bioinfo #38

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Add blast.ml to lib/bioinfo
cecilpert Dec 5, 2017
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Add selectors to re-use prokka outputs + Modify command line to have …
cecilpert Dec 5, 2017
a4c2242
Revert "Add selectors to re-use prokka outputs + Modify command line …
cecilpert Dec 6, 2017
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72 changes: 72 additions & 0 deletions lib/bioinfo/blast.ml
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open Core
open Bistro.Std
open Bistro.EDSL
open Bistro_bioinfo.Std

type db = [`blast_db] directory
let env = docker_image ~account:"pveber" ~name:"ncbi-blast" ~tag:"2.4.0" ()

let db_name = "db"

let fastadb fa dbtype =
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better call it makedb since it's the name of the tool

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also dbtype should be the first argument and named

workflow ~descr:"blast.makedb" [
mkdir_p dest ;
cmd ~env "makeblastdb" [
opt "-in" dep fa ;
opt "-dbtype" ident dbtype ;
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the type of dbtype is Bistro.Template.t, which is really not convenient for a user. I'd much prefer have a polymorphic variant type here [nucl | prot]

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So we have to create the type ? In the .ml ? I don't really see how to call the function then.
Something like type polymorphic_variant = Prot | Nucl in .ml and call Blast.makedb ~dbtype:Prot ref_prot outside ? With a "reconversion" to string somewhere to call the command line.
(it's not exactly like that because it's not working)

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actually if you use polymorphic variants `Nucl and `Prot, you don't need to declare the type and it's also easier when calling the function. So yes, basically a call would be just like you say Blast.makedb ~dbtype:`Prot ref_prot, and yes you have to provide the conversion function that will take a variant and make an appropriate Bistro.Template.t out of it.

opt "-out" ident (dest // db_name) ;
] ;
]

(* Basic blastn*)

let blastn ?evalue ?word_size ?task ?gapopen ?gapextend ?penalty
?reward ?outfmt ?perc_identity ?qcov_hsp_perc ?max_hsps ?max_target_seqs ?(threads = 4) db query out_name = (*See blastn documentation to know what options are*)
workflow ~descr:"blastn" ~np:threads [
mkdir_p dest ;
cmd "blastn" ~env [
opt "-db" ident (dep db // db_name) ;
opt "-query" dep query ;
opt "-out" ident (dest // out_name) ;
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what's the motivation for creating a directory here? Couldn't we give dest to the -out option?

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Because it's already created in makedb ? Or do we have to create it in the main pipeline ?

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Well yes, the same could be said about the database, I think in both cases you don't really need to create a directory and put the resulting file in it. The resulting file should be put at the location dest directly I think.

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To be more precise in think your wrapper could be simplified like this:

opt "-db" dep db ;
opt "-out" ident dest ;

of course the wrapper for makedb should be modified accordingly.

option (opt "-evalue" float) evalue ;
option (opt "-word_size" int) word_size ;
option (opt "-task" string) task ;
option (opt "-gapopen" int) gapopen ;
option (opt "-gapextend" int) gapextend ;
option (opt "-penalty" int) penalty ;
option (opt "-reward" int) reward ;
option (opt "-outfmt" string) outfmt ;
option (opt "-perc_identity" float) perc_identity ;
option (opt "-qcov_hsp_perc" float) qcov_hsp_perc ;
option (opt "-max_hsps" int) max_hsps ;
option (opt "-max_target_seqs" int) max_target_seqs ;
opt "-num_threads" ident np ;
]
]

let blastp ?evalue ?word_size ?task ?gapopen ?gapextend ?penalty
?reward ?outfmt ?perc_identity ?qcov_hsp_perc ?max_hsps ?max_target_seqs ?(threads = 4) db query out_name = (*See blastn documentation to know what options are*)
workflow ~descr:"blastp" ~np:threads [
mkdir_p dest ;
cmd "blastp" ~env [
opt "-db" ident (dep db // db_name) ;
opt "-query" dep query ;
opt "-out" ident (dest // out_name) ;
option (opt "-evalue" float) evalue ;
option (opt "-word_size" int) word_size ;
option (opt "-task" string) task ;
option (opt "-gapopen" int) gapopen ;
option (opt "-gapextend" int) gapextend ;
option (opt "-penalty" int) penalty ;
option (opt "-reward" int) reward ;
option (opt "-outfmt" string) outfmt ;
option (opt "-perc_identity" float) perc_identity ;
option (opt "-qcov_hsp_perc" float) qcov_hsp_perc ;
option (opt "-max_hsps" int) max_hsps ;
option (opt "-max_target_seqs" int) max_target_seqs ;
opt "-num_threads" ident np ;
]
]