add a new workflow: fna2faa

lib/bppsuite.ml

@@ -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

@@ -6,3 +6,7 @@ val bppseqgen :
   nb_sites:int ->
   tree:nhx workflow ->
   nucleotide_fasta workflow
+
+val fna2faa :
+  fna:nucleotide_fasta workflow ->
+  aminoacid_fasta workflow