File Coverage

blib/lib/CracTools/SAMReader.pm

Criterion	Covered	Total	%
statement	67	87	77.0
branch	16	36	44.4
condition	2	3	66.6
subroutine	12	14	85.7
pod	9	9	100.0
total	106	149	71.1

###############################################################################
#                                                                             #
#    Copyright © 2012-2013 -- IRB/INSERM                                      #
#                            (Institut de Recherche en Biothérapie /          #
#                             Institut National de la Santé et de la          #
#                             Recherche Médicale)                             #
#                                                                             #
#  Auteurs/Authors:  Jerôme AUDOUX              #
#                    Nicolas PHILIPPE             #
#                                                                             #
#  -------------------------------------------------------------------------  #
#                                                                             #
#  Ce fichier fait partie de la suite CracTools qui contient plusieurs pipeline#
#  intégrés permettant de traiter les évênements biologiques présents dans du #
#  RNA-Seq. Les CracTools travaillent à partir d'un fichier SAM de CRAC et d'un#
#  fichier d'annotation au format GFF3.                                       #
#                                                                             #
#  Ce logiciel est régi  par la licence CeCILL  soumise au droit français et  #
#  respectant les principes  de diffusion des logiciels libres.  Vous pouvez  #
#  utiliser, modifier et/ou redistribuer ce programme sous les conditions de  #
#  la licence CeCILL  telle que diffusée par le CEA,  le CNRS et l'INRIA sur  #
#  le site "http://www.cecill.info".                                          #
#                                                                             #
#  En contrepartie de l'accessibilité au code source et des droits de copie,  #
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#  pris connaissance  de la licence CeCILL,  et que vous en avez accepté les  #
#  termes.                                                                    #
#                                                                             #
#  -------------------------------------------------------------------------  #
#                                                                             #
#  This file is part of the CracTools which provide several integrated        #
#  pipeline to analyze biological events present in RNA-Seq data. CracTools   #
#  work on a SAM file generated by CRAC and an annotation file in GFF3 format.#
#                                                                             #
#  This software is governed by the CeCILL license under French law and       #
#  abiding by the rules of distribution of free software. You can use,        #
#  modify and/ or redistribute the software under the terms of the CeCILL     #
#  license as circulated by CEA, CNRS and INRIA at the following URL          #
#  "http://www.cecill.info".                                                  #
#                                                                             #
#  As a counterpart to the access to the source code and rights to copy,      #
#  modify and redistribute granted by the license, users are provided only    #
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#  The fact that you are presently reading this means that you have had       #
#  knowledge of the CeCILL license and that you accept its terms.             #
#                                                                             #
###############################################################################

=encoding utf8

=head1 NAME

CracTools::SAMReader - An easy to use tool to read files in SAM format.

=head1 SYNOPSIS

  use CracTools::SAMReader;

  # Creating the reader
  my $sam_reader = CracTools::SAMreader->new($sam,'CRAC');

  # Get an iterator to go through the SAM file in a linear way
  my $it = $sam_reader->iterator();

  # Iterate on lines and explore CRAC special fields of SAM
  while(my $line = $it->()) {
    if(defined $line->events('Junction') && $line->isClassified('normal')) {
      my @junctions = @{$line->events('Junction')};
      foreach my $junction (@junctions) {
        print "Foud Junction : [type : $junction->{type}, loc : $junction->{loc}, gap : $junction->{gap}]\n";
      }
    }
  }

=head1 DESCRIPTION

Reader for SAM format, including CRAC special fields.

=cut

package CracTools::SAMReader;

use strict;
use warnings;
use CracTools::SAMReader::SAMline;

=head1 METHODS

=head2 new

  Arg [1] : String - SAM file
  Arg [2] : (Optional) String - SAM type
            - CRAC
            - CRAC_EMT

  Example     : $reader = CracTools::SAMreader->new('file.sam','CRAC');
  Description : Create a new reader obect
  ReturnType  : CracTools::SAMreader
  Exceptions  : none

=cut

sub new {
  my $class = shift;
  my ($sam_file,$sam_type) = @_;

  my $self = bless{
      sam_file => $sam_file,
      sam_type => $sam_type,
  }, $class;

  $self->init();

  return $self;
}

=head2 iterator

  Example     : my $it = $sam_reader->iterator();
                while(my $line = $it->()) {
                  print $line->seq,"\n";
                }
  Description : Create an iterator to go throud each lines of the file
  ReturnType  : Iterator on CracTools::SAMline
  Exceptions  : none

=cut

sub iterator {
  my $self = shift;
  my $f_it = $self->iteratorFile("IGNORE_HEADERS");

  return sub {
    my ($line) = $f_it->();
    my $sam_line;
    if(defined $line) {
      $sam_line = CracTools::SAMReader::SAMline->new($line);
    }
    return $sam_line;
  };
}

=head2 iteratorFile

  Arg [1] : (Optional) String - options (IGNORE_HEADERS,..)

  Example     : my $it_f = $sam_reader->iteratorFile();
                while(my ($line,$line_number) = $it->()) {
                  print $line,"\n";
                }
  Description : Create an iterator to go throud each lines of the file
  ReturnType  : Iterator on Array (String,Int) where the  is the
                line, and  the line number.
  Exceptions  : none

=cut

sub iteratorFile {
  my $self = shift;
  my $option = shift;
  my $sam_file = $self->{sam_file};

  if($sam_file =~ /\.sam$/) {
    open(SAM,"< $sam_file") or die ("Cannot open $sam_file");
  } elsif($self->{sam_file} =~ /\.sam.gz$/) {
    open(SAM,"gunzip -c $sam_file |") or die ("Cannot open $sam_file");
  } elsif($self->{sam_file} =~ /\.bam$/) {
    open(SAM, "-|", "samtools view -h $sam_file" )or die "Cannot open $sam_file, check if samtools are installed.";
  } else {
    die "Unknown file format. Must be either a BAM or a SAM(.gz)";
  }

  my $next_line;
  my $line_number = 0;

  if(defined $option && $option eq "IGNORE_HEADERS") {
    while(my $line = ) {
      if(!($line =~ /^@/)) {
        $next_line = $line;
        $line_number++;
        last;
      }
    }
  } else {
    $next_line = ;
  }

  return sub {
    my $sam_line = $next_line;
    $next_line = ;
    $line_number++;
    if($sam_line) {
      return $sam_line, $line_number;
    } else {
      return ();
    }
  };
}

=head1 GETTERS AND SETTERS

=cut

=head2 header

  Description : Getter/setter for attribute header
  ReturnType  : none
  Exceptions  : none

=cut

sub header {
  my $self = shift;
  return $self->{header};
}

=head2 refSeqLength

  Description : Return the length of the reference sequence given in argument
  ReturnType  : Integer

=cut

sub refSeqLength {
  my $self = shift;
  my $ref_seq = shift;
  croak("Missing reference sequence name in arguement") unless defined $ref_seq;
  my @header_lines = split('\n',$self->header);
  my $ref_seq_len;
  foreach (@header_lines) {
    if ($_ =~/\@SQ.*SN:$ref_seq/) {
      ($ref_seq_len) = $_ =~ /LN:([^\t]+)/;
    }
  }
  return $ref_seq_len;
}

=head2 commandLine

  Description : Return crac command line defined in SAM's header
  ReturnType  : String

=cut

sub commandLine {
  my $self = shift;
  if(defined $self->header) {
    my @header_lines = split('\n',$self->header);
    my $command_line;
    foreach (@header_lines) {
      if ($_ =~/\@PG.*PN:crac/) {
        ($command_line) = $_ =~ /CL:([^\t]+)/;
      }
    }
    return $command_line;
  } else {
    return undef;
  }
}

=head2 getCracArgumentValue

  Description : Retrun the value of the specified argument in crac command line

=cut

sub getCracArgumentValue {
  my $self = shift;
  my $argument = shift;
  my $command_line = $self->commandLine;
  if(defined $command_line) {
    my ($value) = $command_line =~ /--$argument\s+(\S+)/;
    return $value;
  } else {
    return undef;
  }
}

=head2 hasCracOption

  Description : Return true if crac command line has specified a certain option

=cut

sub hasCracOption {
  my $self = shift;
  my $option = shift;
  croak("Missing argument") unless defined $option;
  if(defined $self->commandLine) {
    return $self->commandLine =~ /--$option/;
  } else {
    return 0;
  }
}

=head1 PRIVATE METHODS

=head2 init (private)

  Description : Initialization method
  ReturnType  : none
  Exceptions  : none

=cut

sub init {
  my $self = shift;
  my $f_it = $self->iteratorFile;
  my $header;
  while(my ($line) = $f_it->()) {
    if($line =~ /^@/) {
      $header .= $line;
    } else {
      last;
    }
  }
  $self->{header} = $header;
}

=head1 AUTHORS

Jerome AUDOUX ELE.

=head1 COPYRIGHT AND LICENSE

Copyright (C) 2012-2013 -- IRB/INSERM
                           (Institut de Recherche en Biothérapie /
                            Institut National de la Santé et de la
                            Recherche Médicale)
                           LIRMM/UM2
                           (Laboratoire d'Informatique, de Robotique et de
                            Microélectronique de Montpellier /
                            Université de Montpellier 2)

=head2 FRENCH

Ce fichier  fait partie  du Pipeline  de traitement  de données NGS de la
plateforme ATGC labélisée par le GiS IBiSA.

Ce logiciel est régi  par la licence CeCILL  soumise au droit français et
respectant les principes  de diffusion des logiciels libres.  Vous pouvez
utiliser, modifier et/ou redistribuer ce programme sous les conditions de
la licence CeCILL  telle que diffusée par le CEA,  le CNRS et l'INRIA sur
le site "http://www.cecill.info".

=head2 ENGLISH

This File is part of the NGS data processing Pipeline of the ATGC
accredited by the IBiSA GiS.

This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".

=cut

1;