rdat2csv.pl

#!/usr/bin/env perl
#===============================================================================
#
#         FILE: rdat2csv.pl
#
#        USAGE: ./rdat2csv.pl  
#
#  DESCRIPTION: 
#
#      OPTIONS: ---
# REQUIREMENTS: ---
#         BUGS: ---
#        NOTES: ---
#       AUTHOR: Christoph Kaempf (CK), kaempf@bioinf.uni-leipzig.de
# ORGANIZATION: 
#      VERSION: 1.0
#      CREATED: 05.08.2012 15:28:44
#     REVISION: ---
#===============================================================================

## Loading modules and initializing variables ##
use strict;
use warnings;
use utf8;
use Data::Dumper;
use File::Basename;
use File::Find;
use Getopt::Long;
use Log::Log4perl qw(get_logger :levels);
use Path::Class;
use Pod::Usage;
my $module_dir = dirname(__FILE__);
push(@INC, $module_dir);

## Configure Getopt::Long ##
Getopt::Long::Configure ("bundling");
#my @files = ();
#my @directories = ();
my $rdat = "";
my $blat = "";
my $help = 0;
my $man = 0;
my $verbose = 0;
my $to_dna = 0;
GetOptions(
#    "file|f=s" => \@files,
#    "directory|d=s" => \@directories,
    "rdat=s" => \$rdat,
    "blat=s" => \$blat,
    "toDNA|t" => \$to_dna,
    "help|h" => \$help,
    "man|m" => \$man,
    "verbose|v+" => \$verbose);

pod2usage(-verbose => 1) && exit if ( $help );
pod2usage(-verbose => 2) && exit if ( $man );
pod2usage({-verbose => 1, -message => "Use this script like this:\n"}) &&
    exit if ( $help || $rdat eq "" || $blat eq "" );

###############################################################################
#                 
# Logger initiation  
#                 
###############################################################################

my $log4perl_conf = file(dirname(__FILE__), "RNAprobing.log.conf");

# Apply configuration to the logger
Log::Log4perl->init("$log4perl_conf");

# Get the logger
my $logger_name = "RNAprobing";
my $logger = &configureLogger($verbose, $logger_name);

$logger->info("++++ ".__FILE__." has been started. ++++");

###############################################################################
#
# Load own perl modules
#
###############################################################################

require RNAprobing::RDATFile;
require RNAprobing::BLASTresult;

##  - check found files and add them to $rdat_files (array reference) if they passed the checks
my $rdat_files = &checkFiles([$rdat]);
my $blat_files = &checkFiles([$blat]);

for (my $i = 0; $i < @{$rdat_files}; $i++ ){
#foreach my $rdat_file ( @{ $rdat_files } ) {
    my $rdat_file = $rdat_files->[$i];
    my $blat_file = $blat_files->[$i];


    # generate output file name
    my($filename, $directories, $suffix) = fileparse($rdat_file);
    my $csv_file = $directories.$filename;
    $csv_file =~ s/\.rdat$/.csv/g;
    # read in BLAST results
    my $blast_object = RNAprobing::BLASTresult->new($blat_file);
    my $query_start = $blast_object->query_start()->[0] - 1;
    my $query_end = $blast_object->query_end()->[0] - 1;
    # read in RDAT file and process information
    my $rdat_object = RNAprobing::RDATFile->new($rdat_file);
    my @sequence = split(//, $rdat_object->sequence());
    my $startpos = $rdat_object->seq_startpos() + $query_start;
    $logger->debug("Startpos: ".$startpos." nt: ".$rdat_object->offset_sequence_map()->{$startpos});
    my $endpos = $startpos + $query_end;
    $logger->debug("Endpos: ".$endpos." nt: ".$rdat_object->offset_sequence_map()->{$endpos});
    my $header = "Position\tNucleotide";
    foreach my $index ( @{$rdat_object->data()->indices()} ) {
        $header .= "\texpReac$index\tscaReac$index";
    }
    $header .= "\n";
    my $lines = "";
    for (my $i = $startpos; $i <= $endpos; $i++ ) {

    	$lines .= $i."\t".$rdat_object->offset_sequence_map()->{$i};
	    foreach my $index ( @{$rdat_object->data()->indices()} ) {
	        if (defined $rdat_object->seqpos_reactivity_map($index)->{$i}){
	         	$lines .= "\t".$rdat_object->seqpos_reactivity_map($index)->{$i};
	        } else {
    	    	$lines .= "\t"
	        }
	        if ( defined $rdat_object->seqpos_non_negative_reactivity_map($index)->{$i}){
	    	$lines .= "\t"
	    	    .$rdat_object->seqpos_non_negative_reactivity_map($index)->{$i};
	        } else {
	    	$lines .= "\t";
	        }
	    }
	    $lines .= "\n";
    }
    $logger->info($lines);
    open(my $csv_fh, ">", $csv_file) or die("Can't open $csv_file.");
    print $csv_fh $header;
    print $csv_fh $lines;
    close($csv_fh);
}
my $j = 0;
foreach my $i ( @{$rdat_files}) {
    $j++;
    $logger->info($j.". processed RDAT file: ".$i);
}
###############################################################
##              
##              Subroutine section
##
###############################################################

###############################################################
##              
##  Invocation - \&wanted
##      - Subroutine used by File::Find
##
###############################################################

#sub wanted {
#    my $logger = get_logger("RNAprobing");
#    $logger->info("$_ is a directory") if ( -d $_ );
#    $logger->info("$_ isn't a directory") unless ( -d $_ );
#    if ( $_ =~ /\.rdat$/ ) {
#        $logger->info($File::Find::name." is a .rdat file");
#        # @files is a global variable
#        push(@files, $File::Find::name);
#    } else {
#        $logger->info("$_ is not a .rdat file");
#    }
#}

###############################################################
##
## &configureLogger($verbosityLevel)
## - Configures and initialzes the Logger
## - $verbosityLevel = scalar value that sets log level
## -- 0 => $ERROR
## -- 1 => $WARN
## -- 2 => $INFO
## -- >2 => $DEBUG
## 
###############################################################

sub configureLogger{
    ## Configure the logger ##
    my $verbose = shift;
    my $logger_name = shift;
    my $logger = get_logger($logger_name);
    $logger->info("Verbosity level: $verbose");
    SELECT:{
	    if ($verbose == 0){$logger->level($ERROR); $logger->debug("Log level is ERROR") ;  last SELECT; }
	    if ($verbose == 1){ $logger->level($WARN) ; $logger->debug("Log level is WARN") ; last SELECT; }
	    if ($verbose == 2){ $logger->level($INFO) ; $logger->debug("Log level is INFO") ; last SELECT; }
	    else { $logger->level($DEBUG); $logger->debug("Log level is DEBUG") ;  last SELECT; }
    }
    return $logger;
}

###############################################################
##
## &checkFiles(@filesToBeChecked)
## - Performs file checks and returns an array with all succesfully checked files
## - @filesToBeChecked = array of files to be checked
##
###############################################################

sub checkFiles {
    my $testfiles = shift;
    my @checkedfiles = ();
    my $logger = get_logger("RNAprobing");
    foreach my $testfile (@{ $testfiles}) {
        $logger->info("Perform file checks for file $testfile");
        if ( -f $testfile ){
            $logger->info("$testfile is a plain file");
            if ( -r $testfile) {
                my $abs_path = File::Spec->rel2abs( $testfile );
                $logger->info("$testfile can be accessed");
                push(@checkedfiles, $abs_path );
                $logger->debug("Absolute path: $abs_path");
            } else {
                $logger->error("Can not access $testfile");
            }
        } else {
            $logger->error("$_ is not a plain file");
            $logger->error("$_ is a directory") if ( -d $testfile);
        }
    }
    return \@checkedfiles;
}

__END__


=head1 NAME

rdat2csv.pl - Creating .csv files fom .rdat files

=head1 SYNOPSIS

rdat2fasta.pl --rdat=</path/to/file> --blat=</path/to/rdat-directory/> -v -t

=head1 DESCRIPTION

B<rdat2fasta.pl> takes RDAT files as input or searches given directories for them and converts them to FASTA files. The FASTA files are created within the same directory as the original RDAT files.

=head1 OPTIONS

=over 4

=item --rdat=</path/to/file.rdat>

RDAT file(s) to be converted to CSV files. Option can be given multiple times.

=item --blat=</path/to/file.blat>

File containing BLAT mapping results.

=item -t, --toDNA

If set RNA sequences are converted into DNA sequences. The resulting file ends on ".dna.fa".

=item -v, --verbose

Increases verbosity level. Option can be given multiple times.

=item -h, --help

Prints the help page.

=item -m, --man

Prints the manual page.

=back

=cut