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https://github.com/jhu99/localali

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https://github.com/jhu99/localali

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README 

        
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PROGRAM: LocalAli

AUTHOR: Jialu Hu

EMAIL: [email protected]



Copyright (C) <2014>  



This program is free software: you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation, either version 3 of the License, or

(at your option) any later version.



This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

GNU General Public License for more details.



You should have received a copy of the GNU General Public License

along with this program.  If not, see .



################################################################################

Description

This file is README file of the package of LocalAli developed by Jialu Hu.

To guide you quickly starting to use our alignment tool, we structured this README into five parts:

1) PREREQUISITE

2) DOWNLOAD

3) COMPILING

4) OPTION

5) EXAMPLES

Before running this program, you are recommended to read this file carefully.

For easy to explain, we denote $LOCALALI as the path to LocalAli folder.



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PREREQUISITE

1. LEMON Graph Library 1.2.3

The source code is freely available under Boost Software License, Version 1.0 at the website: http://ftp.mi.fu-berlin.de/jhu/LocalAli/lemon-1.2.3.tar.gz

Please first compile the lemon graph library before compiling the code of LocalAli.

Note that this package should be moved to the directory $LOCALALI/include.

2. GoTermFinder

This package is necessary only if you want to use "-analyse" option to analyze the Gene Ontology enrichment of reported alignments.

It can be download at http://search.cpan.org/dist/GO-TermFinder/lib/GO/TermFinder.pm.



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DOWNLOAD

1. Checkout the source code from the project's subversion repository

svn checkout http://localali.googlecode.com/svn/trunk/ $LOCALALI



2. Download datasets and lemon-1.2.3

datsets: http://ftp.mi.fu-berlin.de/jhu/LocalAli/dataset.tar.gz

lemon-1.2.3: http://ftp.mi.fu-berlin.de/jhu/LocalAli/lemon-1.2.3.tar.gz



Download the datasets into the folder $LOCALALI and uncompress it with command:

cd $LOCALALI

tar -zxvf dataset.tar.gz

Download lemon-1.2.3 into the folder $LOCALALI/include/ and uncompress it with command:

cd $LOCALALI/include

tar -zxvf lemon-1.2.3.tar.gz



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COMPILING

The compiler g++-4.6 as well as its higher variants is strongly recommended to compile the source code, but not limited to. Visual Studio 11 is also supported.

The compilation should be done under Linux and Mac OS X with several simple commands as follows:



1. Compile LEMON GRAPH LIBRARY



cd $LOCALALI/include/lemon-1.2.3/

./configure

./make

./make check (optional)

./make install (optional)



2. Compile LOCALALI



cd $LOCALALI

./make MODE=Release

#If you want to compile it in Debug mode, run command:

./make (MODE=Debug)

#The binary code will be in the folder ./$LOCALALI after compilation.



#if you want to compile it with other compilers such as g++-4.7, do it like this:

./make MODE=Release CXX=g++-4.7



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OPTION

You can see the detailed option information with option "-h".

It is noted that there are two options you must specify if you want to run LOCALALI for an alignment task. They are described as follows:



1. -profile

The default file is "./profile.txt", but you can also change the filename and path by "-profile" option.

This file tells the program where to find the input files.

It is expected to be in two-column tab-delimited format.

These lines starting with "#" will be seen as comments.

Each line has one keyword and one value, like this:

$keyword	$value

Using this file, you are allowed to set keywords (folder species layers tree) here.



For example:



--------------BEGIN OF PROFILE--------------

folder ./dataset/3-way/

species Celeg20130707

species Dmela20130707

species Scere20130707

layers  input_blast.txt

tree    tree.txt

--------------END OF PROFILE--------------



The specified filenames which are required by localali are:

./dataset/3-way/Celeg201300707.txt

./dataset/3-way/Dmela20130707.txt

./dataset/3-way/Scere20130707.txt

./dataset/3-way/input_blast.txt

./dataset/3-way/tree.txt



Interactions of each species are in three-column tab-delimited format (INTERACTOR_A INTERACTOR_B score) as follows (the third column is not necessary):

--------------BEGIN OF NETWORK--------------

O43521	Q07820	0.40

P05556	P07948	0.43

P05556	P13612	0.66

P07948	P13612	0.43

2609382	P40763	0.40

P17947	Q15156	0.54

--------------END OF NETWORK--------------



The layered graph will be constructed through these homologous proteins (with evalue <1e-07). It looks as follows (the third column is not necessary):

--------------BEGIN OF HOMOLOGY--------------

P31946	Q20655	9e-146

P31946	P41932	2e-137

P62258	Q20655	5e-121

P41932	P62258	5e-113

Q04917	Q20655	9e-133

P41932	Q04917	1e-126

P61981	Q20655	2e-132

P41932	P61981	8e-129

P27348	Q20655	4e-138

P27348	P41932	2e-132

--------------END OF HOMOLOGY--------------



2. other option in Usage



Usage:

  ./localali -version|-alignment|-analyse|-format [--help|-h|-help]

     [-alpha num] [-beta num] [-extdist1 int] [-extdist2 int]

     [-formatfile str] [-maxext int] [-method int] [-minext int]

     [-numconnected int] [-numseeds int] [-numspecies int]

     [-numspinetries int] [-numthreads int] [-parallel] [-profile str]

     [-resultfolder str] [-score_threshold num] [-seedrep int]

     [-seedsize int] [-seedtries int] [-task int] [-verbose int]

Where:

  --help|-h|-help

     Print a short help message

  -alignment

     Execute the alignment algorithm.

  -alpha num

     Impact factor of the evolutionary rate. Default is 0.2

  -analyse

     Make analysis on the alignment results.

  -beta num

     The second impact factor of the evolutionary rate of interactions. Default is 2.0.

  -extdist1 int

     Distance of neighbors in the search for seeds. Default is 1.

  -extdist2 int

     Distance of neighbors in the search for subnets. Default is 2.

  -format

     Process input or output file into proper format.

  -formatfile str

     Input file which is used to analyse the quality of alignments.

  -maxext int

     Maximal number of the extension. Default is 13.

  -method int

     Specify the method used for verification. LocalAli 1, NetworkBlastM 2. Default is 1.

  -minext int

     Minimal number of the extension. Default is 3.

  -numconnected int

     Number of connected subnetwork. Default is 3.

  -numseeds int

     Number of refined seeds. Default is 400.

  -numspecies int

     Number of the species compared. Default is 3.

  -numspinetries int

     Number of tries for strongly connected spines. Default is 5.

  -numthreads int

     Number of threads. Default is 1.

  -parallel

     Run LocalAli in parallel if it is true. Default is false.

  -profile str

     Configuration of various input parameters. Default is "./profile.txt".

  -resultfolder str

     Configuration of various input parameters.

  -score_threshold num

     Score threshold of subnets which are qualified. Default is 0.2.

  -seedrep int

     Allow protein replicatioin in refined seeds. Default is false.

  -seedsize int

     Size of the seeds. Default is 2.

  -seedtries int

     Number of tries for each refined seeds. Default is 1.

  -task int

     Specify the task of each method. Default is 0.

  -verbose int

     Display standard output levle:0-3. Default is 0.

  -version

     Show the version number.



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EXAMPLES



cd $LOCALALI

mkdir ./result 

# The alignment results will be in this folder.



Perform LocalAli on a test alignment (human-worm-fly) with command:



mkdir ./result/3-way

mkdir ./result/3-way/alignments

set the directory of the dataset in ./profile/profile_test.txt.

./localali -alignment -parallel -numthreads 16 -numspinetries 20 -numspecies 3 -numseeds 2000 -score_threshold 0.3 -resultfolder ./result/3-way -seedtries 2 -minext 3 -maxext 13 -profile ./profile/profile_test.txt -verbose 1 -extdist1 2 -extdist2 2 -seedrep 1 



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END

THANKS FOR READING

If you have any questions regarding to the program, please don't hesitate to contact us through email.