[Bioperl-l] strand in Bio::SearchIO when parsing fasta35 output

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Mon Oct 26 13:04:08 EDT 2009

Dear all

Where does this go?  Perhaps I am doing something wrong.

Fasta35 output puts the strand in the hit list at the top:

cluster_99033:3                                (  23) [r]  115 37.9  0.0011
cluster_79238:1                 (  27) [f]  126 38.0 0.00097 0.963 0.963   27

The [r] stands for reverse and the [f] stands for forward.

There is also the text "rev-comp" after the hit line further down.

However, when I parse fasta35 output using SearchIO and output the strand of the HSP:

print $hsp->strand('hit'), ",";
print $hsp->strand('query'), "\n";

This simply prints out 0, 0 (I assume 0 is the default in BioPerl for "I don't know which strand it's on").

So the information is there, but it's not getting parsed.  Alternatively, I've missed something and will feel a bit foolish.

Currently using BioPerl 1.6.0


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