TreeGrafter: a new software tool for annotating uncharacterized protein sequences using annotated phylogenetic trees.

Copyright (C) 2017 Paul Thomas This file may be copied and redistributed freely, without advance permission, provided that this Copyright statement is reproduced with each copy.

LIMITATION OF WARRANTY NOTHING IN THIS AGREEMENT WILL BE CONSTRUED AS A REPRESENTATION MADE OR WARRANTY GIVEN BY PAUL THOMAS OR ANY THIRD PARTY THAT THE USE OF DATA PROVIDED HEREUNDER WILL NOT INFRINGE ANY PATENT, COPYRIGHT, TRADEMARK OR OTHER RIGHTS OF ANY THIRD PARTY. DATA IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND WHATSOEVER, EXPRESS OR IMPLIED, INCLUDING IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. PAUL THOMAS MAKES NO WARRANTY THAT ITS DATA DOES NOT CONTAIN ERRORS.

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TreeGrafter - Version 1.01

TreeGrafter is a new software tool for annotating uncharacterized protein sequences, using annotated phylogenetic trees.

The scripts are located in: https://github.com/haimingt/TreeGrafter

The PANTHER data for this tool is located in: ftp://ftp.pantherdb.org/downloads/TreeGrafter/

June 11, 2018

Software authors: Haiming Tang, Robert D Finn

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Installing and running TreeGrafter

As a Docker container

TreeGrafter can be run using the Docker container (Docker container author: Aleksandra Tarkowska)

The Docker container is available in https://hub.docker.com/r/ningzhithm/treegrafter/

Docker installation instructions for Windows, OSX and Linux platforms are available on https://docs.docker.com/install/.

Run software in container

Pull Docker container and run test

$ docker run --rm --name treegrafter -v /path/to/output:/output ningzhithm/treegrafter:1.01 -f ./Test/sample.fasta -o /output/sample.1.out -d ./Test/PANTHER_mini -auto
Unable to find image 'ningzhithm/treegrafter:1.01' locally
1.01: Pulling from ningzhithm/treegrafter
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Digest: sha256:85fb4be0512140c50838155f70a8ba3fdcc7556e0c1e9cd519cdc5ac0e382610
Status: Downloaded newer image for ningzhithm/treegrafter:1.01
Reading HMM file
hmm database size in memory: 10640
fasta file size in memory: 10816
Best algorithm is hmmsearch

PANTHER DB can be mounted as a data volume using -v /path/to/treeGrafter1.01_supplemental:/opt/supplemental

$ docker run --rm --name treegrafter -v /path/to/sample:/sample -v /path/to/output:/output -v /path/to/treeGrafter1.01_supplemental:/opt/supplemental ningzhithm/treegrafter:1.01 -f /sample/sample.fasta -o /output/sample.1.out -d /opt/supplemental -auto

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As a local Perl script

Software dependencies

• RAxML 8.2.4 available at https://github.com/stamatak/standard-RAxML
• HMMER 3.1b2 available at http://hmmer.org/download.html
• Perl
• Perl modules:
  • Bio::TreeIO available at http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz
  • Try::Tiny available at http://search.cpan.org/~ether/Try-Tiny-0.28/lib/Try/Tiny.pm
  • JSON::Parse available at http://search.cpan.org/~bkb/JSON-Parse-0.49/lib/JSON/Parse.pod
  • IO::String available at http://search.cpan.org/~gaas/IO-String-1.08/String.pm

When using Perl scripts it can be challenging to install all of the dependencies and there can be "drift" in functionality of the external Perl modules that this script was originally written for. To migate this, we have generate a standalone executable that contain all of the dependencies.

OS X

If you are using OSX, you can skip installing the Perl modules, and use the executable directly.

Windows

If you are using Windows, you can use Cygwin to run the tool. You follow the additional steps below:

1. Install Cygwin and Perl

• Install Cygwin from https://cygwin.com/install.html,
• Install “Perl” and “make” in “Select Packages” while running “setup.exe”.

2. Open Cygwin and verify Perl installation with command: % perl -v.
3. Install Cpanminus http://search.cpan.org/~miyagawa/App-cpanminus-1.7040/lib/App/cpanminus.pm#Installing_to_system_perl. Cpanminus could be installed using command cpan App::cpanmius
4. Install required modules: Try::Tiny, BioPerl, JSON::Parse, IO::String, using commands below:

   % cpanm Try::Tiny 
   % cpanm Bio::Perl 
   % cpanm JSON::Parse 
   % cpanm IO::String 
   

The location to Perl and Perl modules must be defined in your $PATH variable. If you have any questions on how to set up $PATH, please contact your UNIX system administrator.

The locations of RAxML and HMMER are required as input for this tool if not defined in $PATH.

Data dependencies:

Download the PANTHER data

% wget  ftp://ftp.pantherdb.org/downloads/TreeMethod/treeGrafter1.01_supplemental.tar.gz

Uncompress the PANTHER data

% tar xvfz treeGrafter1.01_supplemental.tar.gz

Download or clone the treeGrafter from github Go to https://github.com/haimingt/TreeGrafting

% cd treeGrafting-master
% perl treeGrafter.pl -f <input fasta file> -o <output file> -d <directory path to treeGrafter1.01_supplemental> -r <optional: RAxML location> -algo <hmmsearch or hmmscan> -auto <Please specify either -algo <hmmscan|hmmsearch> or -auto, but not both> -k <keep temporary files: 1 for yes> -hmmer <for previously stored output of hmmscan or hmmsearch>

Examples:

1. using the Test data, automatically choose hmmscan or hmmsearch:

   cd treeGrafting-master
   perl treeGrafter.pl -f ./Test/sample.fasta -o ./Test/sample.1.out -d ./Test/PANTHER_mini -auto
   

2. using the prevously stored hmmscan output

   IMPORTANT! provide -algo hmmscan for hmmscan.out; -algo hmmsearch for hmmsearch.out

   perl treeGrafter.pl -f ./Test/sample.fasta -o ./Test/sample.2.out -d ./Test/PANTHER_mini -algo hmmscan -hmmer ./Test/sample.fasta.hmmscan.out
   

3. using hmmsearch algo

   perl treeGrafter.pl -f ./Test/sample.fasta -o ./Test/sample.3.out -d ./Test/PANTHER_mini -algo hmmsearch
   

4. using the full dataset treeGrafter1.01_supplemental

   perl treeGrafter.pl -f ./Test/sample.fasta -o ./Test/sample.4.out -d ./path/to/treeGrafter1.01_supplemental -algo hmmsearch
   

5. using the executable on mac

   treeGrafter.osx -f ./Test/sample.fasta -o ./Test/sample.5.out -d ./path/to/treeGrafter1.01_supplemental -algo hmmsearch
   

The input file must be a list of sequences in fasta format

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TreeGrafter Input and Output formats

Sample input fasta file:

sample.fasta

>STRCO|Gene=CAB44512|UniProtKB=Q9XAS3
--DRTAYSLVATDLDGTLLRGDDTVSDRSLAALARVAGAGARHLVVTGRPAPRVRPLLDRLGCTGLAVCGQGAQVYDAGH
RMLWSVTLDRELAETALGIEAEVGQVHAAVDQDGVTP-----DYLMPHPTAVRVERRAQLWS-TPISKVLLR-HPELTDD
ELAATARAVVGSLATVTMSGPGTVELQPCGITKATGLALAAEHLGLERRRTIAFGDMPNDIPMFQWAAHGVAMAGAHPEL
KAVADEVTTTNEDDGVAVVLERIF--
>STAA8|EnsemblGenome=SAOUHSC_02831|UniProtKB=Q2FVA2
------VKAIAVDMDGTFLDSKKTYDKLRFEAITELRNRDITFIAASGNQYAKLKSIFGDRD--MYFISENGAVIYNG--
NELYNKSFNRQVFQQVVDLNMKQSIDQLVICGKH-TAF--KEDTRFYYHQLKEIDSLQQLPE-DDYVKIAFNIN-RETHP
NVDEEVATQFSNDIKLVSSGHDSIDIIMPNMTKGQALKRLLDKWEMSPSELMAFGDANNDKDMLAFAKHSYVMENSHDEE
LNIASAVAPSNDKQGVLTIIEQ----

Sample output info:

sample.ouput

STRCO_Gene_CAB44512_UniProtKB_Q9XAS3	PTHR10000	SF:PTHR10000:SF8;NAME:Sugar phosphatase YidA; GO-Annotations:GO:0016311;GO:0016791;GO:0005737;
STRR6_EnsemblGenome_spr1125_UniProtKB_Q8DPK0		PTHR10000		    SF:PTHR10000:SF27;NAME:5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YbjI;GO-Annotations:GO:0016311;GO:0016791;GO:0005737;

Output format, separated by tab:
first column: gene id (non word characters replaced by '_'); second column: best-matched PANTHER family third column: predicted SF and GO annotations for the gene id

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Troubleshooting:

If you have any problems, please contact us at: [email protected]

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