From 5d20e0a7e3331cd574a9f3531d801c0798a26423 Mon Sep 17 00:00:00 2001 From: Olga Tsiouri Date: Wed, 18 Nov 2020 22:35:15 +0200 Subject: [PATCH] Add files via upload --- pdb_corner/pdb_chain_to_fasta.jl | 33 ++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 pdb_corner/pdb_chain_to_fasta.jl diff --git a/pdb_corner/pdb_chain_to_fasta.jl b/pdb_corner/pdb_chain_to_fasta.jl new file mode 100644 index 0000000..b3ca7b1 --- /dev/null +++ b/pdb_corner/pdb_chain_to_fasta.jl @@ -0,0 +1,33 @@ +# 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() \ No newline at end of file