Information about get_input_for_LOX.pl Perl script.


FOLDER CONTENT:
    - 'get_input_for_LOX.pl' is the perl script to create the LOX input file.
    - 'some_yeast_CDS.txt' is a file with a few CDSs from 'Saccharomyces cerevisiae' in FASTA format
        to be used as example.
    - 's1_ELAND.txt', 's2_ELAND.txt', 's3_ELAND.txt' and 's4_ELAND.txt' are faked ELAND output 
        files. Some of the short reads in these files match the yeast CDSs from 'some_yeast_CDS.txt' file.  


OVERVIEW:
    This is a utility to create the input file for LOX software.
    To create the input file, the script uses the output files from the ELAND
    software. ELAND is a short-read aligner part of the Illumina/Solexa suite.
    This script only considers the unique exact matches from Eland output.
    After the name of the Perl script, the user needs to indicate a list of 
    input files.
    The first file should be the CDS of the genome (fasta format).
    This is the file used by the Perl script to census the short reads.
    The rest of files should be the ELAND output files.
    Each ELAND output file should correspond to a different 
    treatment.
    Although the application only considers the unique exact matches from
    ELAND, it does not discard the possibility of multiple matching against CDSs.
    Multiple matching can occur if ELAND matched the short reads against a 
    genome sequence and CDS for that genome has overlapping CDSs (like yeast).
    Reads with multiple matches will be excluded to produce the LOX input.
 

HOW TO RUN IT:
    To run this script you need Perl installed in your computer.
    Perl runs on most platforms (including Windows) and comes by default in most Linux 
    distributions and Mac OS X.
    You will run the script using the example files from the terminal in UNIX environment 
    (like Linux or MacOS X) typing the following:  
    ./get_input_for_LOX.pl some_yeast_CDS.txt s1_ELAND.txt s2_ELAND.txt s3_ELAND.txt s4_ELAND.txt
    
    or: 

    perl get_input_for_LOX.pl some_yeast_CDS.txt s1_ELAND.txt s2_ELAND.txt s3_ELAND.txt s4_ELAND.txt


OUTPUT: 
    The Perl script creates an output file named 'LOXinputfile.txt' with the sequence census. 
    The census output produced using the example files is identical to the 'LOXinputfile.txt' 
    file in the 'example' folder, except for the first three rows (header rows). 
    The first row contains the ELAND filenames as headers for each column. 
    The second and third row NEED TO BE CHANGED manually (editing the file with any text editor), 
    to indicate the methodology (#2) and treatment (#3) information. 
    While the first row is designated for user use only, these two last rows are used by the LOX program to calculate
    the results. 
    Thus, the same methodology/treatment abbreviation must be used for each identical methodology/treatment type.
    As an example, if in two experiments were cells grown in minimal media and we use the code MM 
    for that, both columns in the third row should have that code exactly. 


SPEED:
    Be forwarned this simple script can take up to several days to produce a LOX input file with millions of unique exact 
    matches and thousands of CDSs.
    The script outputs the progress based on the number of short reads per each ELAND file.
    To improve speed, the script should be parallelized. 
    Each ELAND file can be run in a different CPU.  Then, the user can put together the different outputs in 
    spreadsheet software, saving the file as tabulated table.

