Bio::Assembly::IO::phrap(3)

NAME
Bio::Assembly::IO::phrap - driver to load phrap.out files.

SYNOPSIS
    # Building an input stream
    use Bio::Assembly::IO;

    # Assembly loading methods
    my $io = Bio::Assembly::IO->new( -file   => 'results.phrap',
                                     -format => 'phrap');

    # Read the entire scaffold
    my $scaffold = $io->next_assembly;

    # Or read one contig at a time to save resources
    while ( my $contig = $io->next_contig ) {
      # Do something ...
    }

DESCRIPTION
This package was developed to load the phrap.out files from the (phred/phrap/consed) package by Phill Green. This files contain just the messages printed to standard out by phrap when building an assembly. This output is redirected by phredPhrap perl-script to a file in the project's directory and hold some bit of information regarding assembly quality, connections between contigs and clone's position inside contigs. It should be noted that such files have no data about the sequence. neither for contig consensus nor for any aligned sequence. Anyway, such information may be loaded from Fasta files in the projects directory and added to the assembly object later.

Note that, because no sequence is loaded for the contig consensus and locations for aligned sequences are only given in "ungapped consensus" coordinates in a phrap.out file, you can't make coordinate changes in assemblies loaded by pharp.pm, unless you add an aligned coordinates for each sequence to each contig's features collection yourself. See Bio::Assembly::Contig::Coordinate_Systems and Bio::Assembly::Contig::Feature_collection..

This driver also loads singlets into the assembly contigs as Bio::Assembly::Singlet objects, although without their sequence strings. It also adds a feature for the entire sequence, thus storing the singlet length in its end position, and adds a tag '_nof_trimmed_nonX' to the feature, which stores the number of non-vector bases in the singlet.

  Implementation
Assemblies are loaded into Bio::Assembly::Scaffold objects composed by Bio::Assembly::Contig objects. No features are added to Bio::Assembly::Contig "_aligned_coord:$seqID" feature class, therefore you can't make coordinate changes in contigs loaded by this module. Contig objects created by this module will have the following special feature classes, identified by their primary tags, in their features collection:

"_main_contig_feature:$ID" : main feature for contig $ID. This
                        feature is used to store information
                        about the entire consensus
                        sequence. This feature always start at
                        base 1 and its end position is the
                        consensus sequence length. A tag,
                        'trimmed_length' holds the length of the
                        trimmed good quality region inside the
                        consensus sequence.

"_covered_region:$index" : coordinates for valid clones inside the
                        contig. $index is the covered region
                        number, starting at 1 for the covered
                        region closest to the consensus sequence
                        first base.

"_unalign_coord:$seqID" : location of a sequence in "ungapped
                        consensus" coordinates (consensus
                        sequence without gaps). Primary and
                        secondary scores, indel and
                        substitutions statistics are stored as
                        feature tags.

"_internal_clones:$cloneID" : clones inside contigs $cloneID should be
                        used as the unique id for each
                        clone. These features have six tags:
                        '_1st_name', which is the id of the
                        upstream (5') aligned sequence
                        delimiting the clone; '_1st_strand', the
                        upstream sequence strand in the
                        alignment; '_2nd_name', downstream (3')
                        sequence id; '_2nd_strand', the
                        downstream sequence strand in the
                        alignment; '_length', unaligned clone
                        length; '_rejected', a boolean flag,
                        which is false if the clone is valid and
                        true if it was rejected.

All coordinates for the features above are expressed as "ungapped consensus" coordinates (See Bio::Assembly::Contig::Coordinate_Systems..

  Feature collection
#

FEEDBACK

  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.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  Support
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 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 the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Robson Francisco de Souza
Email rfsouza@citri.iq.usp.br

head1 APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Parser methods

  next_assembly
 Title   : next_assembly
 Usage   : $scaffold = $stream->next_assembly()
 Function: returns the next assembly in the stream
 Returns : a Bio::Assembly::Scaffold object
 Args    : none

  next_contig
 Title   : next_contig
 Usage   : $scaffold = $stream->next_contig()
 Function: Returns the next contig or singlet in the PHRAP stream.
 Returns : a Bio::Assembly::Contig or Bio::Assembly::Single object
 Args    : none

  scaffold_annotations
 Title   : scaffold_annotations
 Usage   : $stream->scaffold_annotations($scaffold)
 Function: Adds ssembly and contig annotations to a scaffold. In the PHRAP
           format, this is the section starting with "INTERNAL"
 Returns : 1 for success
 Args    : a Bio::Assembly::Scaffold object to attach the annotations to

  write_assembly (NOT IMPLEMENTED)
    Title   : write_assembly
    Usage   : $ass_io->write_assembly($assembly)
    Function: Write the assembly object in Phrap compatible ACE format
    Returns : 1 on success, 0 for error
    Args    : A Bio::Assembly::Scaffold object