diff variant_effect_predictor/Bio/Assembly/IO.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Assembly/IO.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,229 @@
+# $Id: IO.pm,v 1.1 2002/11/04 11:47:49 heikki Exp $
+#
+# BioPerl module for Bio::Assembly::IO
+#
+#   based on the Bio::SeqIO module
+#       by Ewan Birney <[e-mail]>
+#       and Lincoln Stein  <[e-mail]>
+#
+# Copyright Robson Francisco de Souza
+#
+# You may distribute this module under the same terms as perl itself
+#
+# _history
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Assembly::IO - Handler for Assembly::IO Formats
+
+=head1 SYNOPSIS
+
+    use Bio::Assembly::IO;
+
+    $in  = Bio::Assembly::IO->new(-file=>"<inputfilename",
+                                -format=>'phrap');
+    $out = Bio::Assembly::IO->new(-file=>">outputfilename",
+                                -format=>'phrap');
+
+    while ( my $seq = $in->next_seq() ) {
+       $out->write_seq($seq);
+    }
+
+=head1 DESCRIPTION
+
+Bio::Assembly::IO is a handler module for formats in the Assembly::IO set
+(e.g. Bio::Assembly::IO::phrap).
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to the
+Bioperl mailing lists  Your participation is much appreciated.
+
+  [e-mail]                 - General discussion
+  http://bio.perl.org/MailList.html     - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+the bugs and their resolution.  Bug reports can be submitted via email
+or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR
+
+Robson Francisco de Souza
+
+E-mail: [e-mail]
+
+=head1 CONTRIBUTORS
+
+#
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+package Bio::Assembly::IO;
+
+use Bio::Root::Root;
+use Bio::Root::IO;
+
+use strict;
+use vars qw(@ISA);
+
+@ISA = qw(Bio::Root::Root Bio::Root::IO);
+
+=head2 new
+
+ Title   : new
+ Usage   : Bio::Assembly::IO->new(-file =>$filename,-format=>'format')
+ Function: Returns a new assembly stream
+ Returns : A Bio::Assembly::IO::Handler initialised 
+           with the appropriate format
+ Args    : -file => $filename
+           -format => format
+
+=cut
+
+sub new {
+    my ($caller,@args) = @_;
+    my $class = ref($caller) || $caller;
+    
+    # or do we want to call SUPER on an object if $caller is an
+    # object?
+    if( $class =~ /Bio::Assembly::IO::(\S+)/ ) {
+	my ($self) = $class->SUPER::new(@args);	
+	$self->_initialize(@args);
+	return $self;
+    } else { 
+
+	my %param = @args;
+	@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
+
+	$class->throw("Need at least a file name to proceed!")
+	    unless (defined $param{'-file'} || defined $ARGV[0]);
+
+	my $format = $param{'-format'} || 
+	    $class->_guess_format( $param{-file} || $ARGV[0] );
+	$format = "\L$format";	# normalize capitalization to lower case
+
+	# normalize capitalization
+	return undef unless( $class->_load_format_module($format) );
+	return "Bio::Assembly::IO::$format"->new(@args);
+    }
+}
+
+# _initialize is chained for all SeqIO classes
+
+sub _initialize {
+    my($self, @args) = @_;
+    # initialize the IO part
+    $self->_initialize_io(@args);
+}
+
+=head2 next_assembly
+
+ Title   : next_assembly
+ Usage   : $cluster = $stream->next_assembly()
+ Function: Reads the next assembly object from the stream and returns it.
+ Returns : a Bio::Assembly::ScaffoldI compliant object
+ Args    : none
+
+=cut
+
+sub next_assembly {
+   my ($self, $seq) = @_;
+   $self->throw("Sorry, you cannot read from a generic Bio::Assembly::IO object.");
+}
+
+
+=head2 _load_format_module
+
+ Title   : _load_format_module
+ Usage   : *INTERNAL Assembly::IO stuff*
+ Function: Loads up (like use) a module at run time on demand
+ Example :
+ Returns :
+ Args    :
+
+=cut
+
+sub _load_format_module {
+  my ($self,$format) = @_;
+  my $module = "Bio::Assembly::IO::" . $format;
+  my $ok;
+
+  eval {
+      $ok = $self->_load_module($module);
+  };
+  if ( $@ ) {
+    print STDERR <<END;
+$self: could not load $format - for more details on supported formats please see the Assembly::IO docs
+Exception $@
+END
+  ;
+  }
+  return $ok;
+}
+
+=head2 _guess_format
+
+ Title   : _guess_format
+ Usage   : $obj->_guess_format($filename)
+ Function: guess format based on file suffix
+ Example :
+ Returns : guessed format of filename (lower case)
+ Args    :
+ Notes   : formats that _filehandle() will guess includes
+           only phrap, by now.
+
+=cut
+
+sub _guess_format {
+   my $class = shift;
+   my $arg   = shift;
+
+   return unless defined($arg);
+   return 'ace' if ($arg =~ /\.ace\.\d+$/i);
+   return 'phrap' if ($arg =~ /\.phrap\.out$/i);
+}
+
+sub DESTROY {
+    my $self = shift;
+
+    $self->close();
+}
+
+# I need some direction on these!! The module works so I haven't fiddled with them!
+# Me neither! (rfsouza)
+
+sub TIEHANDLE {
+    my ($class,$val) = @_;
+    return bless {'seqio' => $val}, $class;
+}
+
+sub READLINE {
+  my $self = shift;
+  return $self->{'seqio'}->next_seq() unless wantarray;
+  my (@list, $obj);
+  push @list, $obj while $obj = $self->{'seqio'}->next_seq();
+  return @list;
+}
+
+sub PRINT {
+  my $self = shift;
+  $self->{'seqio'}->write_seq(@_);
+}
+
+1;
+