[BioRuby] spidey parser
GOTO Naohisa
ngoto at gen-info.osaka-u.ac.jp
Wed Nov 8 15:04:00 UTC 2006
Hi,
To get Bio::Spidey::Report::SegmentPair objects, you can use
Bio::Spidey::Report::Hit#each (iterates over each exon segment pair),
Bio::Spidey::Report::Hit#hsps (gets an array of exon segment pairs),
Bio::Spidey::Report::Hit#exons (same as hsps), or
Bio::Spidey::Report::Hit#segmentpairs (gets an array of all segment
pairs including introns) methods.
small sample code:
--------------------------------------------------
require 'bio'
Bio::FlatFile.open('file.spidey') do |ff|
ff.each do |entry|
entry.each do |hit|
p hit.query_def # query=mRNA definition
p hit.target_def # target=genomic sequence definition
hit.each do |hsp|
p hsp.qseq # query=mRNA sequence (with gaps)
p hsp.midline # middle line
p hsp.hseq # hit=genomic sequence (with gaps)
p hsp.aaseqline # amino acid sequence line
end
end
end
end
--------------------------------------------------
Thanks,
Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
Department of Genome Informatics, Genome Information Research Center,
Research Institute for Microbial Diseases, Osaka University, Japan
On Wed, 8 Nov 2006 14:20:08 -0000
"jan aerts \(RI\)" <jan.aerts at bbsrc.ac.uk> wrote:
> All,
>
> I'm trying to use the spidey parser (Bio::Spidey) to find mismatches in
> the sequence between mRNA and genomic sequence. For example the C/T
> mismatch at the end of the last line in the snippet below.
>
> <SNIP>
> Exon 3: 46694102-46690011 (gen) 152-4244 (mRNA)
>
> TATTTTGCAGATAAGTCATCATGGTGAAAAGCCACATAGGCAGTTGGATCCTGGTTCTCT
> ||||||||||||||||||||||||||||||||||||||||||||||||||
> ATAAGTCATCATGGTGAAAAGCCACATAGGCAGTTGGATCCTGGTTCTCT
> V I M V K S H I G S W I L V L
>
>
> ACAGGCCAGTGGATCAGTATAGTAACCAGAACAACTTTGTGCATGACTGTGTCAACATCA
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
> ACAGGCCAGTGGATCAGTATAGTAACCAGAACAACTTTGTGCATGACTGTGTCAATATCA
> Y R P V D Q Y S N Q N N F V H D C V N I
> </SNIP>
>
> I couldn't find out exactly how to walk through all segments of the
> alignment and get to the midline. The
> Bio::Spidey::Report::SegmentPair#initialize method in the
> bio/appl/spidey/report.rb file mentions that it "is designed to be
> called from Bio::Spidey::Report::* classes." and that "users shall not
> call it directly."
>
> How can I walk over all segment pairs and access the mRNA and genomic
> sequences as well as the midline?
>
> Many thanks,
>
> Dr Jan Aerts
> Bioinformatics Group
> Roslin Institute
> Roslin, Scotland, UK
> +44 131 527 4200
>
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