Provided by: libbio-perl-perl_1.7.2-3_all bug


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


           # 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 ...


       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, 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

       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

       "_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


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AUTHOR - Robson Francisco de Souza


       head1 APPENDIX

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

Parser methods

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

        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

        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