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Ace/Sequence.pm  view on Meta::CPAN

	       ['OFFSET','OFF'],
	       ['LENGTH','LEN'],
	       'REFSEQ',
	       ['DATABASE','DB'],
	      ],@_);

  # Object must have a parent sequence and/or a reference
  # sequence.  In some cases, the parent sequence will be the
  # object itself.  The reference sequence is used to set up
  # the frame of reference for the coordinate system.

  # fetch the sequence object if we don't have it already
  croak "Please provide either a Sequence object or a database and name"
    unless ref($seq) || ($seq && $db);

  # convert start into offset
  $offset = $start - 1 if defined($start) and !defined($offset);

  # convert stop/end into length
  $length = ($end > $start) ? $end - $offset : $end - $offset - 2
    if defined($end) && !defined($length);

  # if just a string is passed, try to fetch a Sequence object
  my $obj = ref($seq) ? $seq : $db->fetch('Sequence'=>$seq);
  unless ($obj) {
    Ace->error("No Sequence named $obj found in database");
    return;
  }

  # get parent coordinates and length of this sequence
  # the parent is an Ace Sequence object in the "+" strand
  my ($parent,$p_offset,$p_length,$strand) = find_parent($obj);
  return unless $parent;

  # handle negative strands
  my $r_strand = $strand;
  my $r_offset = $p_offset;
  $offset ||= 0;
  $offset *= -1 if $strand < 0;

  # handle feature objects
  $offset += $obj->offset if $obj->can('smapped');

  # get source
  my $source = $obj->can('smapped') ? $obj->source : $obj;

  # store the object into our instance variables
  my $self = bless {
		    obj        => $source,
		    offset     => $offset,
		    length     => $length || $p_length,
		    parent     => $parent,
		    p_offset   => $p_offset,
		    refseq     => [$source,$r_offset,$r_strand],
		    strand     => $strand,
		    absolute   => 0,
		    automerge  => 1,
		   },$pack;

  # set the reference sequence
  eval { $self->refseq($refseq) } or return if defined $refseq;

  # wheww!
  return $self;
}

# return the "source" object that the user offset from
sub source {
  $_[0]->{obj};
}

# return the parent object
sub parent { $_[0]->{parent} }

# return the length
#sub length { $_[0]->{length} }
sub length { 
  my $self = shift;
  my ($start,$end) = ($self->start,$self->end);
  return $end - $start + ($end > $start ? 1 : -1);  # for stupid 1-based adjustments
}

sub reversed {  return shift->strand < 0; }

sub automerge {
  my $self = shift;
  my $d = $self->{automerge};
  $self->{automerge} = shift if @_;
  $d;
}

# return reference sequence
sub refseq {
  my $self = shift;
  my $prev = $self->{refseq};
  if (@_) {
    my $refseq = shift;
    my $arrayref;

  BLOCK: {
      last BLOCK unless defined ($refseq);

      if (ref($refseq) && ref($refseq) eq 'ARRAY') {
	$arrayref = $refseq;
	last BLOCK;
      }

      if (ref($refseq) && ($refseq->can('smapped'))) {
	croak "Reference sequence has no common ancestor with sequence"
	  unless $self->parent eq $refseq->parent;
	my ($a,$b,$c) = @{$refseq->{refseq}};
	#	$b += $refseq->offset;
	$b += $refseq->offset;
	$arrayref = [$refseq,$b,$refseq->strand];
	last BLOCK;
      }


      # look up reference sequence in database if we aren't given
      # database object already
      $refseq = $self->db->fetch('Sequence' => $refseq)

Ace/Sequence.pm  view on Meta::CPAN

  return ($tl,$offset,$strand < 0 ? ($length,'-1') : ($length,'+1') ) if $length;
}

sub _get_toplevel {
  my $obj = shift;
  my $class = $obj->class;
  my $name  = $obj->name;

  my $smap = $obj->db->raw_query("gif smap -from $class:$name");
  my ($parent,$pstart,$pstop,$tstart,$tstop,$map_type) = 
    $smap =~ /^SMAP\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(.+)/;

  $parent ||= '';
  $parent =~ s/^Sequence://;  # remove this in next version of Acedb
  return ($parent,$pstart,$pstop);
}

# create subroutine that filters GFF files for certain feature types
sub _make_filter {
  my $self = shift;
  my $automerge = $self->automerge;

  # parse out the filter
  my %filter;
  foreach (@_) {
    my ($type,$filter) = split(':',$_,2);
    if ($automerge && lc($type) eq 'transcript') {
      @filter{'exon','intron','Sequence','cds'} = ([undef],[undef],[undef],[undef]);
    } elsif ($automerge && lc($type) eq 'clone') {
      @filter{'Clone_left_end','Clone_right_end','Sequence'} = ([undef],[undef],[undef]);
    } else {
      push @{$filter{$type}},$filter;
    }
  }

  # create pattern-match sub
  my $sub;
  my $promiscuous;  # indicates that there is a subtype without a type

  if (%filter) {
    my $s = "sub { my \@d = split(\"\\t\",\$_[0]);\n";
    for my $type (keys %filter) {
      my $expr;
      my $subtypes = $filter{$type};
      if ($type ne '') {
	for my $st (@$subtypes) {
	  $expr .= defined $st ? "return 1 if \$d[2]=~/$type/i && \$d[1]=~/$st/i;\n"
	                       : "return 1 if \$d[2]=~/$type/i;\n"
	}
      } else {  # no type, only subtypes
	$promiscuous++;
	for my $st (@$subtypes) {
	  next unless defined $st;
	  $expr .= "return 1 if \$d[1]=~/$st/i;\n";
	}
      }
      $s .= $expr;
    }
    $s .= "return;\n }";

    $sub = eval $s;
    croak $@ if $@;
  } else {
    $sub = sub { 1; }
  }
  return ($sub,$promiscuous ? [] : [keys %filter]);
}

# turn a GFF file and a filter into a list of Ace::Sequence::Feature objects
sub _make_features {
  my $self = shift;
  my ($gff,$filter) = @_;

  my ($r,$r_offset,$r_strand) = $self->refseq;
  my $parent = $self->parent;
  my $abs    = $self->absolute;
  if ($abs) {
    $r_offset  = 0;
    $r = $parent;
    $r_strand = '+1';
  }
  my @features = map {Ace::Sequence::Feature->new($parent,$r,$r_offset,$r_strand,$abs,$_)}
                 grep !m@^(?:\#|//)@ && $filter->($_),split("\n",$gff);
}


# low level GFF call, no changing absolute to relative coordinates
sub _gff {
  my $self = shift;
  my ($opt,$db) = @_;
  my $data = $self->_query("seqfeatures -version 2 $opt",$db);
  $data =~ s/\0+\Z//;
  return $data; #blasted nulls!
}

# shortcut for running a gif query
sub _query {
  my $self = shift;
  my $command = shift;
  my $db      = shift || $self->db;

  my $parent = $self->parent;
  my $start = $self->start(1);
  my $end   = $self->end(1);
  ($start,$end) = ($end,$start) if $start > $end;  #flippity floppity

  my $coord   = "-coords $start $end";

  # BAD BAD HACK ALERT - CHECKS THE QUERY THAT IS PASSED DOWN
  # ALSO MAKES THINGS INCOMPATIBLE WITH PRIOR 4.9 servers.
#  my $opt     = $command =~ /seqfeatures/ ? '-nodna' : '';
  my $opt = '-noclip';

  my $query = "gif seqget $parent $opt $coord ; $command";
  warn $query if $self->debug;

  return $db->raw_query("gif seqget $parent $opt $coord ; $command");
}

# utility function -- reverse complement
sub _complement {