Hi,
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
wiki(
http://gmod.org/wiki/Load_BLAST_Into_Chado#Convert_BLAST_analysis_to_GFF3)
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.
thanks,
-siddhartha
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