Bioperl: Another problem, this one uglier.

[carl virtanen]

Hi.
Still haven't figured out what was happening in the last problem i had, but i
managed a sort of unelegant work around. 
But here's something i don't understand. I have a bunch of blast reports
(2.0.10) in a single file. Some are hits, some are misses. Now, i use the
example program thusly:

cat myblast.reports | perl parse_blast.pl -table 1

everything works, and it has extracted a nice looking table of all the hits in
my blast file. Only one problem.... The query names DO NOT match with the
correct subjects (ie-sequence identifiers-column 3).  Actually, this problem is
related to my earlier problem  i think (actually, i know it is).  Say for
example you have a blast file with reports like this:
Blast 1 report->has hits
Blast 2 report->no hits
Blast 3 report->no hits
Blast 4 report-> has hits

Now, the BioBlast picks up the first hits. Then it skips the next 2 reports (no
hits) and picks up the Blast 4 report. Ok. Only problem, is that the query name
reported in the table is picked up off of Blast 2 and NOT Blast 4, which is the
correct query name for that set of hits.  This is a major problem. At least for
me!  If i'm doing something wrong here in my parsing, let me know. Better yet,
let everybody know EXACTLY what must be done. The worst thing is to get results,
that look ok but which are wrong.

Carl
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