[Bioperl-l] No hits/hsps are displayed while rendering image using Bio::Graphics (parsed blast+ tabular output (-m 6 equivalent to legacy blast -m 8) file using Bio::SearchIO)

[sheetal gosrani]

Hi,

I am trying to parse (using Bio::SearchIO) and render (using Bio::Graphics)
the blast output file in tabular format (-m 6 option in blast+ 2.2.23
version which is equivalent to -m 8 in legacy C based blast). I do not get
anything displayed on the image for some reason that I am unable to debug.

I tried to just parse the file using Bio::SearchIO, format => 'blasttable'
and I get this warning message:
--------------------- WARNING ---------------------
MSG: Did not define the number of conserved matches in the HSP; assuming
conserved == identical (19)
---------------------------------------------------
I cannot avoid this message as the information it needs is not in the file.
Is this message causing the hits/hsps to be not displayed ?

Some details on the OS and version:
OS:
$ uname -a
Linux sheetal-ubuntu 2.6.32-27-generic #49-Ubuntu SMP Wed Dec 1 23:52:12 UTC
2010 i686 GNU/Linux

Perl :  v5.10.1 (*) built for i486-linux-gnu-thread-multi

BioPerl Version :
$ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
1.006001

Bio::SearchIO version:
$ perl -MBio::SearchIO -e 'printf "%vd\n", $Bio::SearchIO::VERSION'
49.46.48.48.54.48.48.49

Bio::Graphics version:
$ perl -MBio::Graphics -e 'printf "%vd\n", $Bio::Graphics::VERSION'
50.46.49.56

Can you please let me know where the problem is ?

Attaching the perl file render_blast.pl and sample blast output file. Also
attaching the perl file which just parses the sample blast file using
Bio::SearchIO as I get the warning message when I run that.

Thanks,
Sheetal Gosrani
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# BLASTX 2.2.23+
# Query:  Contig_4
# Database: nr
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 6 hits found
Contig_4	gi|189485521|ref|YP_001956462.1|	47.50	40	20	1	271	387	405	444	4e-008	44.3
Contig_4	gi|189485521|ref|YP_001956462.1|	58.33	36	14	1	113	217	351	386	4e-008	38.9
Contig_4	gi|15605800|ref|NP_213177.1|	59.52	42	17	0	271	396	380	421	4e-008	58.5
Contig_4	gi|15605800|ref|NP_213177.1|	73.33	15	4	0	170	214	346	360	4e-008	24.6
Contig_4	gi|150021420|ref|YP_001306774.1|	54.76	42	18	1	271	396	392	432	7e-008	48.5
Contig_4	gi|150021420|ref|YP_001306774.1|	53.13	32	14	1	122	214	341	372	7e-008	33.9
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