[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
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
More information about the Bioperl-l