nicer function signature for webblast()

docs/webblast.md

@@ -1,19 +1,20 @@
 # WebBLAST
 
-API for Julia to call the BLAST Web API of NCBI and EBI.
+API for Julia to call the BLAST Web API of [NCBI](http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome).
 
 ## Exported functions
 
 #### webblast
 
 ```julia
-webblast(provider::String, sequence::String, threshold::Float64, cached=false)
+webblast(sequence::String, threshold::Float64=0.005, provider::Symbol=:ncbi, cached=false)
 ```
-
 Calls the the API of the given provider to search for a protein sequence and returns all hits within a E-Value threshold.
 
-**provider** A provider for a BLAST REST API, e.g. NCBI/EBI BLAST. Default "ncbi" (EBI to be implemented), "ncbi" searches for the sequence in the PDB.
-
 **sequence** The sequence to search for.
 
-**cached** Default ```false```, results can be cached, for example during development.
+**threshhold** threshold for the E-value of hits to be returned. Default is 0.005.
+
+**provider** A provider for a BLAST REST API, e.g. NCBI/EBI BLAST. Default ``:ncbi` (EBI to be implemented), "ncbi" searches for the sequence in the PDB.
+
+**cached** Default ```false```, results can be cached, for example during development.

src/WebBLAST/WebBLAST.jl

@@ -99,7 +99,7 @@ module WebBLAST
 
   #main()
 
-  function webblast(provider::String, sequence::String, threshold::Float64, cached=false)
+  function webblast(sequence::String, threshold::Float64=0.005, provider::Symbol=:ncbi, cached=false)
       info("Searching for sequence: $(sequence)")
 
       # try to use cached version
@@ -117,7 +117,7 @@ module WebBLAST
       end
 
 
-      if provider == "ncbi"
+      if provider == :ncbi
         rid, rtoe = ncbi_blast_put(sequence)
         info("NCBI rid: $(rid)")
         if ncbi_blast_search_info(rid)

src/pipeline.jl

@@ -24,7 +24,7 @@ FLFLIKHNPTNTIVYFGRYWSP"
 threshold = 0.005
 
 
-results = webblast("ncbi", seq, threshold, true)
+results = webblast(seq, threshold, :ncbi, true)
 
 
 # PDB IDs and Chain IDs
@@ -58,4 +58,4 @@ end
 for struc in structures
 	m = structure_to_matrix(struc)
 	println(size(m))
-end
+end