Merge pull request #3 from jakobnissen/tblastx

Add tblastx

src/NCBIBlast.jl

@@ -4,18 +4,22 @@ export blastn,
        blastp,
        blastx,
        tblastn,
+       tblastx,
        makeblastdb
 
 using CondaPkg
 
-function add_cli_kwargs!(cmd, kwargs)
+function add_cli_kwargs!(cmd::Vector{String}, kwargs)
     for (key,val) in pairs(kwargs)
         if val isa Bool
             val && push!(cmd, string("-", key))
-        elseif val isa AbstractVector
-            append!(cmd, [string("-", key), string.(val)...])
         else
-            append!(cmd, [string("-", key), string(val)])
+            push!(cmd, string("-", key))
+            if val isa AbstractVector
+                append!(cmd, map(string, val))
+            else
+                push!(cmd, string(val))
+            end
         end
     end
 
@@ -261,6 +265,59 @@ function tblastn(stdin = nothing; stdout=stdout, kwargs...)
     end
 end
 
+"""
+    tblastx([input]; stdout, kwargs...)
+
+Run `tblastx` with passed kwargs.
+Use `arg=true` to pass flags
+(eg `lcase_masking=true` will pass `-lcase_masking`).
+
+Optionally, provide an input that will be provided
+as `stdin` (a file string, or `IO` type).
+
+To print results to somewhere other than `stdout`,
+use eg `stdout="results.txt"`.
+
+```julia
+julia> tblastx(; h=true)
+USAGE
+  tblastx [-h] [-help] [-import_search_strategy filename]
+    [-export_search_strategy filename] [-db database_name]
+    [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
+    [-negative_gilist filename] [-negative_seqidlist filename]
+    [-taxids taxids] [-negative_taxids taxids] [-taxidlist filename]
+    [-negative_taxidlist filename] [-no_taxid_expansion]
+    [-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
+    [-db_hard_mask filtering_algorithm] [-subject subject_input_file]
+    [-subject_loc range] [-query input_file] [-out output_file]
+    [-evalue evalue] [-word_size int_value] [-qcov_hsp_perc float_value]
+    [-max_hsps int_value] [-xdrop_ungap float_value] [-searchsp int_value]
+    [-sum_stats bool_value] [-max_intron_length length] [-seg SEG_options]
+    [-soft_masking soft_masking] [-matrix matrix_name]
+    [-threshold float_value] [-culling_limit int_value]
+    [-best_hit_overhang float_value] [-best_hit_score_edge float_value]
+    [-subject_besthit] [-window_size int_value] [-lcase_masking]
+    [-query_loc range] [-strand strand] [-parse_deflines]
+    [-query_gencode int_value] [-db_gencode int_value] [-outfmt format]
+    [-show_gis] [-num_descriptions int_value] [-num_alignments int_value]
+    [-line_length line_length] [-html] [-sorthits sort_hits]
+    [-sorthsps sort_hsps] [-max_target_seqs num_sequences]
+    [-num_threads int_value] [-remote] [-version]
+
+DESCRIPTION
+   Translated Query-Translated Subject BLAST 2.16.0+
+
+Use '-help' to print detailed descriptions of command line arguments
+```
+"""
+function tblastx(stdin = nothing; stdout=stdout, kwargs...)
+    cmd = ["tblastx"]
+    add_cli_kwargs!(cmd, kwargs)
+    CondaPkg.withenv() do
+        run(pipeline(Cmd(cmd); stdout, stdin))
+    end
+end
+
 
 """
     makeblastdb(; kwargs...)