[Bioperl-l] bp_search2gff.pl and strand information

Siddhartha Basu sidd.basu at gmail.com
Tue Oct 20 12:11:12 EDT 2009

The bp_search2gff.pl seems to be not giving out strand information for
hit entries when i am trying a tblastn format conversion. Here is the
test case tried on sample 'tblastn' data file from the latest bioperl.

bp_search2gff.pl -i tblastn.out -o tblastn.gff3 -f blast -t hit \
-s tblastn_test --method match_part --addid --target --version 3

The output ....

gi|10040111|emb|AL390796.6|AL390796	tblastn_test	match_part	7603	7671 34	.	0	ID=HAHU;Target=Sequence:HAHU 56 78;score=34
gi|10040111|emb|AL390796.6|AL390796	tblastn_test	match_part	7069	7152 33	.	0	ID=HAHU;Target=Sequence:HAHU 31 58;score=33
test6	tblastn_test	match_part	3822	3848	30	.	2 ID=HAHU;Target=Sequence:HAHU 72 80;score=30
test6	tblastn_test	match_part	1794	1814	29	.	1 ID=HAHU;Target=Sequence:HAHU 93 99;score=29

I am not sure about the expected behaviour,  but assume it will give out
the strand information for hit as given in the HSP module documentation
and described in the GMOD

One thing that i noticed is in line 237 of the script(bp_search2gff.pl), 
$feature->strand ( $proxyfor->strand * $otherf->strand);
will definitely produce the 0(unknown) for tblastn as the query strand
is 0 for tblastn report. 

So,  is this behaviour is a feature or bug. What am i missing here.


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