[BioRuby] spidey parser
jan aerts (RI)
jan.aerts at bbsrc.ac.uk
Wed Nov 8 14:20:08 UTC 2006
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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