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Initial commit of UniFIRE codebase

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# maven build:
/**/target/
# IntelliJ Idea:
/**/*.iml
/**/*.eml
/.idea
# Eclipse:
/.classpath
/.project
/.settings
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# Changelog
All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
## [Unreleased]
### Added
### Changed
- Replace Null positions by "" in output TSV file
### Removed
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Copyright 2018 European Molecular Biology Laboratory, EMBL-EBI
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
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# UniFIRE Project
UniFIRE (The UniProt Functional annotation Inference Rule Engine) is an engine to execute rules in the UniProt Rule Markup Language (URML) format.
It can be used to execute the UniProt annotation rules (UniRule and SAAS).
This project is a work in progress, open for private collaboration only. Please do not share this code without explicit authorization.
Introducing presentation: [UniFIRE-URML.pptx](misc/media/UniFIRE-URML.pptx)
## Getting Started
### Prerequisites
#### Hardware
A machine with at least 2 Go of memory.
#### Operating system support
The Java software is portable for any system.
Scripts are only provided for Linux and Mac OS.
#### Software
- Java (>=1.8)
### Usage
#### Try it out
We provide some sample files in the [sample](samples) folder to test the software.
**Example with UniRule rules & InterProScan XML input:**
``` bash
$ ./distribution/bin/unifire.sh -r samples/unirule-urml-2019_04.xml -i samples/input_ipr.fasta.xml -t samples/unirule-templates-2019_04.xml -o ~/output_unirule_annotations.csv
```
*Note: To be able to predict the UniRule positional annotations, a template file is provided (`samples/unirule-templates-2018_05.xml`) (optional.)*
**Example with SAAS rules & Fact XML input:**
``` bash
$ ./distribution/bin/unifire.sh -r samples/saas-urml-2019_04.xml -i samples/input_facts.xml -s XML -o ~/output_saas_annotations.csv
```
_Note_: With all rule systems, it is possible that a protein get the exact same annotation from different rules due to overlap in condition spaces.
#### Options
```
usage: unifire -i <INPUT_FILE> -o <OUTPUT_FILE> -r <RULE_URML_FILE> [-f <OUTPUT_FORMAT>] [-n
<INPUT_CHUNK_SIZE>] [-s <INPUT_SOURCE>] [-t <TEMPLATE_FACTS>] [-m <MAX_MEMORY>] [-h]
--------------------------------------------
-i,--input <INPUT_FILE> Input file (path) containing the proteins to annotate
and required data, in the format specified by the -s
option.
-o,--output <OUTPUT_FILE> Output file (path) containing predictions in the format
specified in the -f option.
-r,--rules <RULE_URML_FILE> Rule base file (path) provided by UniProt (e.g UniRule
or SAAS) (format: URML).
-f,--output-format <OUTPUT_FORMAT> Output file format. Supported formats are:
- TSV (Tab-Separated Values)
- XML (URML Fact XML)
(default: TSV).
-n,--chunksize <INPUT_CHUNK_SIZE> Chunk size (number of proteins) to be batch processed
simultaneously
(default: 1000).
-s,--input-source <INPUT_SOURCE> Input source type. Supported input sources are:
- InterProScan (InterProScan Output XML)
- UniParc (UniParc XML)
- XML (Input Fact XML)
(default: InterProScan).
-t,--templates <TEMPLATE_FACTS> UniRule template sequence matches, provided by UniProt
(format: Fact Model XML).
-m <MAX_MEMORY> Max size of the memory allocation pool in MB (JVM -Xmx)
(default: 4096 MB).
-h,--help Print this usage.
```
***
## Data preparation
This section is a walkthrough on how to prepare your data, assuming you are starting from scratch: from a set of sequences (multifasta) that you would like to annotate.
More advanced users / developers with an existing bioinformatics pipeline already integrating InterProScan results should try to load their existing data into the fact model described on the Developer Guide below.
### MultiFasta header format
The MultiFasta headers should, more or less, follow the UniProtKB conventions ([https://www.uniprot.org/help/fasta-headers](https://www.uniprot.org/help/fasta-headers))
The minimal structure of the header is the following:
```
>{id}|{name} {flags}
```
* `{id}` must be a unique string amongst the processed sequences
* `{name}`:
* can be any string starting from the previous separator, that should not contain any flag
* might contains `(Fragment)` if applicable (e.g "`ACN2_ACAGO Acanthoscurrin-2 (Fragment)`")
* `{flags}` \[mandatory]: to be considered a valid header, only the following flags should be provided:
* OX=`{taxonomy Id}`
* `{flags}` \[optional]: If possible / applicable, you should also provide:
* OS=`{organism name}`
* GN=`{recommended gene name}`
* GL=`{recommended ordered locus name (OLN) or Open Reading Frame (OLN) name}`
* OG=`{gene location(s), comma-separated if multiple}` ([cf. organelle ontology](https://www.ebi.ac.uk/ena/WebFeat/qualifiers/organelle.html))
The UniProt header format has been slightly extended with GL and OG flags.
Optionally, `{id}` can be prepended by `{database}|`, to follow UniProt conventions. If used, it will simply be skipped during the parsing.
Also note that any additional flags will also be ignored.
#### Examples of valid headers:
From UniProt:
```
>tr|Q3SA23|Q3SA23_9HIV1 Protein Nef (Fragment) OS=Human immunodeficiency virus 1 OX=11676 GN=nef PE=3 SV=1
```
From UniProt, customized with additional flags:
```
>tr|A0A0D6DT88|A0A0D6DT88_BRADI Maturase K (Fragment) OS=Brachypodium distachyon OX=15368 GN=matK GL=BN3904_34004 OG=Plastid,Chloroplast PE=3 SV=1
```
Customized minimal:
```
>123|Mystery protein OX=62977
```
Customized full:
```
>MyPlantDB|P987|Photosystem II protein D1 OS=Lolium multiflorum OX=4521 GN=psbA GL=LomuCp001 OG=Plastid
```
### Fetching the full lineages
From the previously described multifasta format, you can use the following scripts to fetch the full NCBI taxonomy id lineage.
* [fetchLineageLocal.py](misc/taxonomy/fetchLineageLocal.py) `<input` `<output>` - for large amount of data on multiple species
* [fetchLineageRemote.py](misc/taxonomy/fetchLineageRemote.py) `<input` `<output>` - for one-off usage / few species
Both scripts will simply replace the OX={taxId} by OX={fullLineage}.
Having the full lineage is necessary for the majority of the rules to be executed.
### Validating the MultiFasta file
If you want to ensure the headers are in the correct format, you can run the following script:
``` bash
$ ./distribution/bin/fasta-header-validator.sh multifasta_sequences.fasta
```
You will get an error message if at least one sequence's header is invalid.
The script also print out warnings if an important data (e.g organism name) is missing. The warnings can be ignored.
### Running InterProScan
Once the multifasta file is ready (cf. previous steps), you can find the matches of all sequences using InterProScan.
It is advised to download the last version from [https://www.ebi.ac.uk/interpro/download.html](https://www.ebi.ac.uk/interpro/download.html) and keep it up-to-date.
The output format must be XML to be accepted as a valid input for UniFIRE.
The option `-dp` or `--disable-precalc` must be used to be able to get the sequence alignments (necessary if you are interested by the positional features annotations provided by UniRule).
Command:
``` bash
./interproscan.sh -f xml -dp -i multifasta_sequences.fasta --appl "Hamap,ProSiteProfiles,ProSitePatterns,Pfam,TIGRFAM,SMART,PRINTS,SFLD,CDD,Gene3D,ProDom,PIRSF,PANTHER,SUPERFAMILY"
```
#### Analyses to run
* Hamap
* ProSiteProfiles
* ProSitePatterns
* Pfam
* TIGRFAM
* SMART
* PRINTS
* SFLD
* CDD
* Gene3D
* ProDom
* PIRSF
* PANTHER
* SUPERFAMILY
It is possible to include/exclude some of the analyses by modifying the `--appl` option in the above command. UniFIRE will still be able to process the data.
By excluding some of those analyses, some rules might not be triggered as a result.
If you do not wish to install InterProScan, you can use the [online version](https://www.ebi.ac.uk/interpro/search/sequence-search) and then download the results in XML.
The only limitation is that the online version does not provide the sequence alignments for the matches, making the execution of UniRule positional features impossible (non-positional rules will still be executed).
### Running UniFIRE
Once you get the InterProScan output (by default, it is the name of the input file, appended with .xml), you can use it as a input for UniFIRE (e.g `--input multifasta_sequences.fasta.xml`).
***
## Developer guide
### Fact Model
The fact model is automatically created from the following XML Schema: [urml-facts.xsd](core/src/main/resources/schemas/xsd/urml-facts.xsd)
The corresponding Java classes are built in the [core](core) module under the package `org.uniprot.urml.facts`, after building the project with Maven (or using the `./build.sh` script).
You can use theses classes (described in the UML diagram below) and the container `org.uniprot.urml.facts.FactSet` to load your own data directly into objects (via an ORM or a custom parser).
### Fact Model Diagram
![fact-model-diagram](misc/media/fact-model.png)
### Rule Model
The rule model is described in another XML Schema available here: [urml-rules.xsd](core/src/main/resources/schemas/xsd/urml-rules.xsd)
The corresponding Java classes are built in the [core](core) module under the package `org.uniprot.urml.rules`.
### Building the software
#### Requirement
- Maven (>= 3.0)
- Java (=1.8 required, cf. limitations)
#### Command
``` bash
$ ./build.sh
```
This script is installing some libraries in your local maven repository (temporary solution before publishing the artifacts on a public repository).
Then it runs `mvn clean install`, assembling all the libs and the execution script under `./distribution/target/unifire-distribution/`.
To use the newly built distribution, you will need to run: `./distribution/target/unifire-distribution/bin/unifire.sh` instead.
### Execution
The execution of the rules relies on [Drools](https://www.drools.org), an open-source rule-based technology developed by RedHat.
It is using an optimized version of the [Rete algorithm](https://en.wikipedia.org/wiki/Rete_algorithm) to match facts and rules in a scalable way.
This tool translates the URML rules into the Drools language, converts the input data according to the rule model and execute all the rules to produce a list of protein annotations.
***
## Limitations
### Memory
A minimum of 2 Go of memory is required for this software to run.
For a large number of protein to process, it is advised to split them into chunks of approx. 1000 proteins per rule evaluation to keep the memory usage low.
This is automatically handled by the `-n / --chunksize` option of UniFIRE (by default 1000).
### Java 9 / 10 issues
- For users, the software will be functional under Java 9 or 10, but you will get some warning messages complaining about illegal reflective accesses. You can simply ignore them at the moment.
- For developers, building the software with JDK 9 / 10 is currently not possible because of JAXB Maven plugin issues. Cf:
* https://github.com/highsource/maven-jaxb2-plugin/issues/120
* https://stackoverflow.com/questions/49717155/failed-to-run-custom-xjc-extension-within-cxf-xjc-plugin-on-java-9
Those issues have been raised very recently. The fixes will be applied as soon as there are available.
***
## Issues & Suggestions
Please do not hesitate to raise new issues if you experience any bugs or you have improvement suggestions on the software, the models, the helper scripts, the documentation, etc...
[UniFIRE Issue Tracker](https://gitlabci.ebi.ac.uk/uniprot.aa/UniFIRE/issues)
## Authors
* **Alexandre Renaux**
## Contact
* **UniProt Help** - [help@uniprot.org](mailto:help@uniprot.org)
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#!/usr/bin/env bash
############################################################################
# Copyright (c) 2018 European Molecular Biology Laboratory
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
############################################################################
function backup_file {
filename=$1
if [[ -e ${filename} ]]; then
mv ${filename} ${filename}_
fi
}
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
DISTRIBUTION_DIR="${SCRIPT_DIR}/distribution"
FTP_SRC="http://ftp.ebi.ac.uk/pub/contrib/UniProtKB/UniFIRE/rules/"
pushd ${SCRIPT_DIR} > /dev/null
echo "Building UniFIRE and downloading dependencies..."
mvn clean install -Dmaven.test.skip=true -Dmaven.source.skip=true
cd ${DISTRIBUTION_DIR}
mvn dependency:copy-dependencies
echo "Done building UniFIRE and downloading dependencies."
popd > /dev/null
echo "Downloading rule urml files..."
for i in aa-rules-saas-urml-latest.xml aa-rules-unirule-urml-latest.xml unirule-templates-latest.xml;
do
backup_file ${SCRIPT_DIR}/samples/${i}
wget ${FTP_SRC}/${i} -O ${SCRIPT_DIR}/samples/${i}
done
echo "Done downloading rule urml files."
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<?xml version="1.0" encoding="UTF-8"?>
<!--
~ Copyright (c) 2018 European Molecular Biology Laboratory
~
~ Licensed under the Apache License, Version 2.0 (the "License");
~ you may not use this file except in compliance with the License.
~ You may obtain a copy of the License at
~
~ http://www.apache.org/licenses/LICENSE-2.0
~
~ Unless required by applicable law or agreed to in writing, software
~ distributed under the License is distributed on an "AS IS" BASIS,
~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
~ See the License for the specific language governing permissions and
~ limitations under the License.
-->
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>uk.ac.ebi.uniprot.aa</groupId>
<artifactId>unifire</artifactId>
<version>1.0-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>
<artifactId>unifire-core</artifactId>
<properties>
<reflections.version>0.9.10</reflections.version>
</properties>
<dependencies>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-xjc</artifactId>
</dependency>
<dependency>
<groupId>org.jvnet.jaxb2_commons</groupId>
<artifactId>jaxb2-basics</artifactId>
<exclusions>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.jvnet.jaxb2_commons</groupId>
<artifactId>jaxb2-basics-runtime</artifactId>
</dependency>
<dependency>
<groupId>org.reflections</groupId>
<artifactId>reflections</artifactId>
<version>${reflections.version}</version>
</dependency>
<dependency>
<groupId>javax.activation</groupId>
<artifactId>activation</artifactId>
</dependency>
<!-- CXF plugin - alternative to the JVNET one in case migration to Java 9 is faster -->
<!--<dependency>-->
<!--<groupId>org.apache.cxf.xjcplugins</groupId>-->
<!--<artifactId>cxf-xjc-ts</artifactId>-->
<!--<version>3.2.1</version>-->
<!--</dependency>-->
<!--<dependency>-->
<!--<groupId>org.apache.cxf.xjc-utils</groupId>-->
<!--<artifactId>cxf-xjc-runtime</artifactId>-->
<!--<version>3.2.1</version>-->
<!--<exclusions>-->
<!--<exclusion>-->
<!--<groupId>javax.xml.bind</groupId>-->
<!--<artifactId>jaxb-api</artifactId>-->
<!--</exclusion>-->
<!--</exclusions>-->