JuliaBioUtils

JuliaBioUtils CLI

Installation

To start, add the package from the github repo.

using Pkg
Pkg.add("https://github.com/nas2011/JuliaBioUtils.jl")

The first build is going to be slow as everything is compiling. There are a few large dependencies that I preemptively included as they will be used for future functionality.

The package will run through the build and precompile. Once that is done, use the package and run the install

using JuliaBioUtils
JuliaBioUtils.comonicon_install()

The CLI tool will now be installed in ~/.julia/bin. You can add this to PATH by

export PATH="~/.julia/bin:$PATH"

If you want to permanently add to path, then put the same line above in your .bashrc file

Use

The CLI tool is accessed using the jutils command.

To see available commands:

>jutils -h

  jutils v1.0.0-DEV

Usage

  jutils <command>

Commands

  batchdownload                                             Batch download PDB files

  getpdb                                                    Download the PDB file for a given PDB id.

Flags

  -h, --help                                                Print this help message.
  --version                                                 Print version.

To see help for a specific command do

>jutils getpdb -h

  getpdb <args> [options] [flags]

Args

  <id>                                                      PDB id

Options

  -o, --outDir <arg>                                        Location to save the file.

  -f, --format <arg>                                        PDB, PDBXML, mmCIF, or MMTF. Default = PDB

Flags

  -a, --all                                                 Show all rows of the resulting PDB table. Default is first
                                                            10 rows.

  -h, --help                                                Print this help message.

To download a single PDB

nicks@DESKTOP-L1DPLD7:~$ jutils getpdb 2hbs
[ Info: Downloading file from PDB: 2HBS
ProteinStructure 2HBS.pdb with 1 models, 8 chains (A,B,C,D,E,F,G,H), 1148 residues, 9677 atoms
10×17 DataFrame
 Row │ ishetero  serial  atomname  altlocid  resname  chainid  resnumber  inscode  x        y        z        occupancy  tempfactor  element  charge  modelnumber  isdisorderedatom
     │ Bool      Int64   String    Char      String   String   Int64      Char     Float64  Float64  Float64  Float64    Float64     String   String  Int64        Bool
─────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   1 │    false       1  N                   VAL      A                1            10.39    20.427   13.21         1.0       45.04  N                          1             false
   2 │    false       2  CA                  VAL      A                1            10.59    18.948   13.104        1.0       43.39  C                          1             false
   3 │    false       3  C                   VAL      A                1            12.056   18.656   12.771        1.0       39.8   C                          1             false
   4 │    false       4  O                   VAL      A                1            12.802   19.566   12.422        1.0       41.29  O                          1             false
   5 │    false       5  CB                  VAL      A                1             9.649   18.332   12.032        1.0       45.28  C                          1             false
   6 │    false       6  CG1                 VAL      A                1            10.08    18.742   10.624        1.0       45.97  C                          1             false
   7 │    false       7  CG2                 VAL      A                1             9.596   16.82    12.175        1.0       45.38  C                          1             false
   8 │    false       8  N                   LEU      A                2            12.468   17.396   12.887        1.0       35.63  N                          1             false
   9 │    false       9  CA                  LEU      A                2            13.855   17.027   12.612        1.0       31.33  C                          1             false
  10 │    false      10  C                   LEU      A                2            14.217   17.008   11.138        1.0       29.7   C                          1             false

If you need the entire DataFrame you can pass the -a or -all flag. You can also select a directory to write to using -o <dir> or --outDir <dir> to specify the write out location.

To batch download specify the location of a delimited file with a header of PDB

nicks@DESKTOP-L1DPLD7:~$ jutils batchdownload a.csv
[ Info: Downloading file from PDB: 1EN2
[ Info: Downloading file from PDB: 1ALW
[ Info: Downloading file from PDB: 1AKE

if the delimiter is anything other than “,” then pass the -d <delim> or --delim <delim> arguments. As with the getpdb command, batchdownload allows you to specify the write out location using -o <dir> or --outDir <dir> .