Bio::SeqIO largefasta
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::SeqIO::largefasta - method i/o on very large fasta sequence files
Package variables
No package variables defined.
Included modules
Bio::Seq::SeqFactory
Inherit
Bio::SeqIO
Synopsis
Do not use this module directly. Use it via the Bio::SeqIO class.
Description
This object can transform Bio::Seq objects to and from fasta flat
file databases.
This module handles very large sequence files by using the
Bio::Seq::LargePrimarySeq module to store all the sequence data in
a file. This can be a problem if you have limited disk space on your
computer because this will effectively cause 2 copies of the sequence
file to reside on disk for the life of the
Bio::Seq::LargePrimarySeq object. The default location for this is
specified by the File::Spec->tmpdir routine which is usually /tmp
on UNIX. If a sequence file is larger than the swap space (capacity
of the /tmp dir) this could cause problems for the machine. It is
possible to set the directory where the temporary file is located by
adding the following line to your code BEFORE calling next_seq. See
Bio::Seq::LargePrimarySeq for more information.
    $Bio::Seq::LargePrimarySeq::DEFAULT_TEMP_DIR = 'newdir';
Methods
_initialize
No description
Code
next_seqDescriptionCode
write_seqDescriptionCode
Methods description
next_seqcode    nextTop
 Title   : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : A Bio::Seq::LargePrimarySeq object
Args : NONE
write_seqcodeprevnextTop
 Title   : write_seq
Usage : $stream->write_seq(@seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object
Methods code
_initializedescriptionprevnextTop
sub _initialize {
  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);    
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(Bio::Seq::SeqFactory->new
			      (-verbose => $self->verbose(), 
			       -type => 'Bio::Seq::LargePrimarySeq'));      
  }
}
next_seqdescriptionprevnextTop
sub next_seq {
    my ($self) = @_;
#  local $/ = "\n";
my $largeseq = $self->sequence_factory->create(); my ($id,$fulldesc,$entry); my $count = 0; my $seen = 0; while( defined ($entry = $self->_readline) ) { if( $seen == 1 && $entry =~ /^\s*>/ ) { $self->_pushback($entry); return $largeseq; } # if ( ($entry eq '>') || eof($self->_fh) ) { $seen = 1; next; }
if ( ($entry eq '>') ) { $seen = 1; next; } elsif( $entry =~ /\s*>(.+?)$/ ) { $seen = 1; ($id,$fulldesc) = ($1 =~ /^\s*(\S+)\s*(.*)$/) or $self->warn("Can't parse fasta header"); $largeseq->display_id($id); $largeseq->primary_id($id); $largeseq->desc($fulldesc); } else { $entry =~ s/\s+//g; $largeseq->add_sequence_as_string($entry); } (++$count % 1000 == 0 && $self->verbose() > 0) && print "line $count\n"; } return unless $seen; return $largeseq;
}
write_seqdescriptionprevnextTop
sub write_seq {
   my ($self,@seq) = @_;
   foreach my $seq (@seq) {       
     my $top = $seq->id();
     if ($seq->can('desc') and my $desc = $seq->desc()) {
	 $desc =~ s/\n//g;
	 $top .= " $desc";
     }
     $self->_print (">",$top,"\n");
     my $end = $seq->length();
     my $start = 1;
     while( $start < $end ) {
	 my $stop = $start + $FASTALINELEN - 1;
	 $stop = $end if( $stop > $end );
	 $self->_print($seq->subseq($start,$stop), "\n");
	 $start += $FASTALINELEN;
     }
   }

   $self->flush if $self->_flush_on_write && defined $self->_fh;
   return 1;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORS - Jason StajichTop
Email: jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _