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                       *   HGTFinder README   *
                       *                      *
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           **********************************************
           *   Table of contents                        *
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           *   0 | License                              *
           *   1 | About                                *
           *   2 | Building and Making HGTFinder        *
           *   3 | Prerequisites to Running HGTFinder   *
           *   4 | Using Custom Files                   *
           *   5 | Running HGTFinder                    *
           *   6 | Output                               *
           *   7 | Example Run                          *
           *   8 | FAQ                                  *
           *   9 | Changelog                            *
           **********************************************

0   |   License
****|*************

Copyright <2015-2022> <Yanbin Yin>

All softwares, scripts, and databases linked to HGTFinder are available only to non-profit research communities and non-commercial uses.  HGTFinder is provided "AS IS" and any express or implied warranties, including, but not limited to, to the implied warranty of fitness for a particular purpose, and any representations or warranties regarding the accuracy or utility of this product are disclaimed.  In no event shall Northern Illinois University, The biology department at Northern Illinois University, or Yin Lab, any of their directors, officers, employees, or agents be liable to you or any third party for direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, cost or damages related to your use of name, your procurement of substitute goods or services, your loss of data or profits, or business interruption), however caused and on any theory of liability, whether in contract, strict liability, or tort arising in any way out of the use of this product, even if the user(s) have been advised of the possibility of damage.

By using this software, the user represent and warrant that they are a member of a non-profit research community; that the use of the product will be for non-commercial research purposes only and that the user agrees to the terms and conditions above.  

0.1   |  Changed to MIT License May 26, 2023

Copyright <2023-> <Yanbin Yin>

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.


1   |   About   
****|***********

HGTFinder is a tool that is used to predict horizontally transferred
genes for a single genome based on a normalized bit score (called an 
R-value, or R for short) and a taxonomic distance between the query 
and subject genome.

If you are not patient, please go directly to the end of this file for 
some "Example Run" and check the input options and input file formats.


2   |   Building and Making HGTFinder
****|***********************************

HGTFinder is designed to run on a Unix or Linux environment with 
little to no altering of any code.  The program is written in C++ 
using C++11 libraries, so an updated compiler that supports these
libraries must also be installed (most OSes support this by default).

A bash script is included to compile all the code and create HGTFinder 
and all its associated tools.  It is named make.sh.  To run it, use 
the following commands:

  cd [DIRECTORY CONTAINING THIS README]
  ./make.sh

Replace "[DIRECTORY CONTAINING THIS README]" with the directory name
that this README file is located in.


3   |   Prerequisites to Running HGTFinder
****|****************************************

R is used to run basic statistical computations on X values, so it 
is required to run HGTFinder.  Additionally, you'll need to install
the "qvalue" and "hash" packages in R.

In order to run HGTFinder you'll need a few files and some data for 
it to use.  For the genome you'll be running HGTFinder on, you'll 
need the following files:
    Blast file: blast results (tab delimited, use -outfmt 6 when 
      running blast) from a blast against some database.  Keep in 
      mind that you'll also need some information about this database
      as well (default is NCBI nr, see below for nr.tax file description).  
    Self blast file: blast results (tab delimited) from a blast 
      against itself.  

There are some files required to build the taxonomic tree.  They are 
supplied by this package, though if you are dealing with a query or
subject that isn't on our tree, you may have to add it in manually
into our own trees.  We provide the names and nodes files downloaded 
from NCBI (ftp.ncbi.nih.gov:/pub/taxonomy) which are available at 
bcb.unl.edu/HGTFinder:
    names.dmp: A file delimited by "[tab]|[tab]" where the first 
      column is the tax id and the second is the name of the genome.
      the third column is a descriptor, it's unused by HGTFinder
    nodes.dmp: A file delimited the same way as the names.dmp file.
      The first column is a tax id, the second is its parent (as a
      tax id).  The third column is its rank.  The rest of the data
      is unused (the third column isn't either) and mainly composes 
      of numerical data.  

The final file that is required is based on the database that you
decide to blast against.  Since we use a proprietary format of 
database, you'll need to use our included DBFormatter tool to 
format your database.  The input file for this DBFormatter tool is
simply a multi-lined file where each line has a protein ID (from
the database) and a taxonomic ID associated with the protein ID.  We 
provide an example of such a file, available at bcb.unl.edu/HGTFinder:
    nr.tax

If you decide to use your own custom database, you'll be required
to make your own protein ID to tax ID file (2 column, tab delimited
where the first column is protein ID and second tax ID).  
Additionally, if the tax ID of any genome is not in the names or 
nodes file, you'll have to append to those as well (do NOT replace
them, however!).  You'll also be required to, as stated above, run 
the DBFormatter tool (See section 4 for more information).


4   |   Using Custom Files
****|************************

HGTFinder is designed to be compatible with custom blast databases.
However, you must first format the database to work properly with it.
Steps to do this are below:
  1) Create a tab delimited file that has a protein ID and taxonomic 
     ID on each line separated by a tab (also described above).  Use
     our nr.tax as an example.
  2) Run the DBFormatter tool from this directory using the following
     command:
       ./DBFormater -i [protein tax file] -o [output].hdb
     Replace "[protein tax file]" with the file name of the file you 
     created in step 1 and "[output]" with the name of the name you 
     want to give the database.

HGTFinder, as seen in part (3) allows the use of custom databases
and taxonomic trees.  The file named "fileLocations" allows you to
tell HGTFinder the locations of these custom files.  It is a 
2-column tab delimited file.  Edit either names.dmp, nodes.dmp, or 
nr.hdb to specify the location of your custom files if you choose to
use them (those files should be in the same directory as HGTFinder).

The FindPercentile.R script should not be changed in this file.  It
is part of the inner workings of the HGTFinder script.  


5   |   Running HGTFinder
****|***********************

There are many options in HGTFinder, some options require other
options to be used as well.  Option dependence (what options must be
supplied together) is below the options list.

Option dependence.  Some options are required or go together with
other options.  Below are lists of options that have to be used in
conjunction with one another.  We'll start with the required options
for EVERY run.  Note that square brackets '[]' imply something that
is needed while angled brackets '<>' imply something that is optional

Required Options
    [-d file_name] [-s file_name] [-t tax_id] [-r rvals]

Required Options for clustering
    [<-S stats_file> <-g GFF3_file>]* [<-p p_value> <-q q_value>]* [-h hole_size]
    *One of the two enclosed options us required

These arguments correspond to the following options below, 
respectively:
    [DB Blast]          -d 
    [Self Blast]        -s 
    [taxid]             -t 
    [out prefix]        -o 
    <gff>               -g 
    <cluster hole size> -h
    <Stats file*>       -S
    <p-value cutoff>    -p
    <q-value cutoff>    -q

    *Generated by HGTFinder

A full list of options and their descriptions are below.

-d | --dbBlast
    This option is followed by the file name of the Blast output 
    against the large database.

-s | --selfBlast
    This option is followed by the file name of the Blast output 
    between the query and itself.  

-t | --tax | --taxID
    This option is followed by the tax ID of the query genome.

-r | --rVals | --rVal
    This option is followed by a comma delimited list of numbers
    between 0 and 1.  The represent R-value cutoffs to use while
    HGTFinder is running.  HGTFinder will output three files for
    each cutoff selected.

-o | --out
    This option is followed by a file name prefix to give to all the
    output files of HGTFinder.  The default output prefix is "out".  

-g | --gff | --gffFile
    This option is followed by a name of a GFF3 formatted file.  The
    IDs and names are expected to match those in the blast (or stats)
    file provided.  This option is ONLY used for clustering.

-S | -a | --stats
    This option is followed by a name of a stats file (generated by
    HGT-Finder).  It allows you to bypass the computation of the 
    stat files if you've run HGT-Finder on a dataset before.  This 
    option is ONLY used for clustering.

-h | -holeSize
    This option is followed by an integer > 0.  It determines the 
    largest size of non-HGT genes allowed between every pair of HGT
    genes within a gene cluster.  See example below:

    Say we have the following genes and HGT (denoted by X)
      G1 G2 G3 G4 G5 G6 G7 G8 G9 G10 G11 G12 G13
         X  X        X           X   X       X
    If the hole size was set to 2, then the following clusters would
    result:
      [G2-G6] and [G10-G13] 
    If the hole size was set to 3, the the following clusters would
    result:
      [G2-G13]

-p | --pval
    This option is followed by a floating point (decimal) value > 0.
    It determines what p-value will be used to determine HGT.  All
    genes with p-value < the given value will be determined to be HGT

-q | --qval
    This option is followed by a floating point (decimal) value > 0.
    It determines what q-value will be used to determine HGT.  All
    genes with q-value < the given value will be determined to be HGT


6   |   Output
****|************

HGTFinder will output 3 files for each cutoff selected, they will be
in the form of:
  [Output].[RVal].dist
    This file contains the following columns:
        query gene
        x (transfer index)
        k (number of hit genomes)
        subject
        subject tax id
        D (distance between query and subject)
        R (normalized bit score)
        N (number of taxonomic nodes between common node and root)
        query lineage (with * denoting the common node)
        subject lineage
    The main value from this file would be the transfer index, X.
    Essentially, a higher X relates to a better chance of horizontal
    gene transfer.  X is not guaranteed to be comparable across 
    multiple genomes.
  [Output].[RVal].dist.cut
    This file is used for the "FindPercentile.R" script.  It contains
    a 2-column, tab-delimited file with each line containing a 
    protein ID (from the blast file) and an X value for that protein
    ID.  
  [Output].[RVal].dist.stats
    This is a 4-column, tab-delimited file that contains the 
    following information:
        gene name
        x value
        p value
        q value
"[Output]" is the output you specified with the "-o" option
(see section 5) and "[RVal]" is the R cutoff used for the given file
output specified in the "-r" option (see section 5).  

Additionally, the standard output stream is utilized to display 
warnings.  You can redirect the standard output to a file using 
'> [file]' at the end of a command to mute this (and save it in a 
file).

Also, the error stream is utilized mainly to display progress 
information while the program is running.  You can mute this using
'2> [file]' at the end of the command and save it to a file.

7   |   Example Run
****|*****************

The Sample_Test folder is available for download at bcb.unl.edu/HGTFinder

To run the sample test from the terminal, run:
    ./HGTFinder -d Sample_Test/Aspfl1.blast.out -s Sample_Test/Aspfl1.blast.self -t 332952 -o Sample_Test/TestOut/HGTOut -r 0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9

To run, muting warnings:
    ./HGTFinder -d Sample_Test/Aspfl1.blast.out -s Sample_Test/Aspfl1.blast.self -t 332952 -o Sample_Test/TestOut/HGTOut -r 0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9 > [warning file]

    Insert a file name in place of "[warning file]"

8   |   FAQ
****|*********

Common Errors
  "Error in q$qvalues : $ operator is invalid for atomic vectors"
    Known causes:
    -Cause: Blasts on the DB and self were run with different 
     options.
       Solution: Rerun the blast(s) with matching options.
    -Cause: Self blast contains multiple hits for the same query 
     sequence (where the query = subject) that are subsequences of 
     the query.
       Solution: This is an issue with blast, the only real solution
       would be to remove this sequence from the DB blast file (this
       sequence will not be able to be predicted for HGT).

  Empty pvals file
    Known causes:
      -Cause: Bit scores are not high enough for non-self, subject 
       hits in DB blast for many (or all) queries.
         Solution: Lower R cutoff.

9   |   Changelog
****|***************

2015-28-10
  Initial, public release

2015-29-10
  Updated README file
    -Added new clustering options
    -Removed "Upcoming changes" section
    -Added "FAQ"
    -Added "Changelog" section
  Updated Sample_Test folder (thanks Guy!)
    -Removed symbolic links
    -Included actual blast files
  Bug fixes
    -Outputted warnings about improper R values due to improperly done
     blast outputs (thanks Cedric!)
    -Fixed floating point precision
    -Fixed exponent bit score bug (thanks Cedric!)

2016-13-03
  Updated README file
    -Added licensing information for HGTFinder (thanks Sebastien!)
    -Fixed typos in README (thanks Sebastien!)
    -Added "hash" R package prerequisite (thanks Sebastien!)