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pdb_corner/pdb_chain_to_fasta.jl

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+# julia
+using ArgParse
+using BioStructures
+# input parameters function
+function parse_commandline()
+
+    s = ArgParseSettings(description = "read a pdb file from PDB and convert it to fasta without the need to download it choosing the model and chain")
+    @add_arg_table s begin
+        "--pdb"
+            help = "input pdb ids"
+        "--model"
+            help = "model to make the fasta file for"
+        "--chain"
+            help = "chain in model to make the fasta file for"    
+        "--out"
+            help = "output fasta file"
+    end
+    return parse_args(s)
+end
+
+function main()
+    parsed_args = parse_commandline()
+    println(parsed_args)
+# main
+    downloadpdb(parsed_args["pdb"]) do fp
+        s = read(fp, PDB)
+        open(parsed_args["out"],"a") do io
+            println(io,">",parsed_args["pdb"],"_",parsed_args["chain"],"\n",LongAminoAcidSeq(s[parse(Int, parsed_args["model"])][parsed_args["chain"]], standardselector, gaps=false))
+        end
+    end
+end
+
+main()