bionic (3) Bio::Assembly::IO::phrap.3pm.gz
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