NAME¶
Bio::Assembly::IO::bowtie - An IO module for assemblies in Bowtie format *BETA*
SYNOPSIS¶
$aio = Bio::Assembly::IO( -file => "mybowtie.bowtie",
-index => "myindex",
-format => "bowtie");
$assy = $aio->next_assembly;
DESCRIPTION¶
This is a read-only IO module designed to convert Bowtie
(<
http://bowtie-bio.sourceforge.net/>) formatted alignments to
Bio::Assembly::Scaffold representations, containing Bio::Assembly::Contig and
Bio::Assembly::Singlet objects. It is a wrapper that converts the Bowtie
format to BAM format taken by the Bio::Assembly::IO::sam module which in turn
uses lstein's Bio::DB::Sam to parse binary formatted SAM (.bam) files guided
by a reference sequence fasta database.
Some information is lost in conversion from bowtie format to SAM/BAM format that
is provided by Bowtie using the SAM output option and the conversion to SAM
format from bowtie format is slower than using bowtie's SAM option. If you
plan to use SAM/BAM format it is preferable to use this Bowtie option rather
than convert the format after the fact.
See the Bio::Assembly::IO::sam documentation for relevant details.
DETAILS¶
- •
- Required files
A bowtie (".bowtie") alignment and the bowtie index or fasta file
used to generate the alignment are required.
- •
- Compressed files
...can be specified directly , if IO::Uncompress::Gunzip is installed. Get
it from your local CPAN mirror.
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
list. 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:
L<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 of the bugs
and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Dan Kortschak¶
Email dan.kortschak adelaide.edu.au
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
new()¶
Title : new
Usage : my $obj = new Bio::Assembly::IO::bowtie();
Function: Builds a new Bio::Assembly::IO object
Returns : an instance of Bio::Assembly::IO
Args : hash of options:
-file => bowtie_output_file
-index => bowtie_index or fasta_file used to create index
-no_head => boolean skip SAM header
-no_sq => boolean skip SQ lines of SAM header
Note : bowtie_output and fasta files may be gzipped