updated pipeline

src/pipeline.jl

@@ -4,46 +4,58 @@ using Requests
 using BiomolecularStructures.PDB
 # 1. search for S_0 in PDB
 
-seq = "MNQLQQLQNPGESPPVHPFVAPLSYLLGTWRGQGEGEYPTIPSFRYGEEIRFSHSGKPVIAY"
-threshold = 1.0e-30
+#seq = "MNQLQQLQNPGESPPVHPFVAPLSYLLGTWRGQGEGEYPTIPSFRYGEEIRFSHSGKPVIAY"
 
-info("Searching for sequence: $(seq)")
+#=seq = "MKKQLKYCFF SLFVSLSSIL SSCGSTTFVL ANFESYISPL LLERVQEKHP LTFLTYPSNE
+KLINGFANNT YSVAVASTYA VSELIERDLL SPIDWSQFNL KKSSSSSDKV NNASDAKDLF
+IDSIKEISQQ TKDSKNNELL HWAVPYFLQN LVFVYRGEKI SELEQENVSW TDVIKAIVKH
+KDRFNDNRLV FIDDARTIFS LANIVNTNNN SADVNPKEDG IGYFTNVYES FQRLGLTKSN
+LDSIFVNSDS NIVINELASG RRQGGIVYNG DAVYAALGGD LRDELSEEQI PDGNNFHIVQ
+PKISPVALDL LVINKQQSNF QKEAHEIIFD LALDGADQTK EQLIKTDEEL GTDDEDFYLK
+GAMQNFSYVN YVSPLKVISD PSTGIVSSKK NNAEMKSKQM STDQMTSEKE FDYYTETLKA
+LLEKEDSAEL NENEKKLVET IKKAYTIEKD SSIRWNQLVE KPISPLQRSN LSLSWLDFKL
+HWW" =#
 
-rid, rtoe = ncbi_blast_put(seq)
-info("rid: $(rid)")
-if ncbi_blast_search_info(rid)
+seq = "QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE
+KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTS
+VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP
+FLFLIKHNPTNTIVYFGRYWSP"
 
-  results =  ncbi_blast_get_results(rid, threshold)
-
-  pdbs = (String,String)[]
+threshold = 0.005
 
-  fastastring = ""
-  for result in results
-  	fasta = fastarepresentation(result)
-
-  	accession = split(result.accession, "_")
 
-  	push!(pdbs, (convert(String,accession[1]), convert(String,accession[2])))
+results = webblast("ncbi", seq, threshold, true)
 
-  	fastastring = string(fastastring, ">", fasta[1], "\n", fasta[2], "\n")
-  end
 
-  # 2. Run MAFFT on results
+# PDB IDs and Chain IDs
+pdbs = (String,String)[]
 
-  println(mafft_from_string(fastastring))
+fastastring = ""
+for result in results
+	fasta = fastarepresentation(result)
+
+	accession = split(result.accession, "_")
 
-  # 3. Get PDBs  
-  for pdb in pdbs
-  	if !isreadable(pdb[1])
-  		data = get(string("http://www.rcsb.org/pdb/files/", pdb[1]))
-  		f = open(Pkg.dir("BiomolecularStructures", ".pdbCache", pdb[1]), 'w')
-  		write(f, data.data)
-  	end
-  	println(get_structure(pdb[1]))
-
-  end
+	push!(pdbs, (convert(String,accession[1]), convert(String,accession[2])))
 
-  # 4. Superimpose PDBs (Best Hit as reference?)
+	fastastring = string(fastastring, ">", fasta[1], "\n", fasta[2], "\n")
+end
 
-
+# 2. Run MAFFT on results
+if length(results) > 0
+	print_fasta(mafft_from_string(fastastring))
+end
+
+# 3. Get PDBs  
+
+structures = Any[]
+
+for pdb in pdbs
+  push!(structures, get_structure(get_remote_pdb(pdb[1])))
+end
+
+# 4. Do something with the PDBs (Superimpose, etc)
+for struc in structures
+	m = structure_to_matrix(struc)
+	println(size(m))
 end