[Bioperl-l] blastall output error (not in bioperl)

[Wiepert, Mathieu]

Not sure if anyone cares, but I kept getting an error from a script I was
running.  The error pointed to a line in my blast output file. I went to the
file, and the file was malformed.  I reran the blast outside of bioperl, and
got the same output file.  The error was in the last line of this hsp.

>gb|T53734.1|T53734 ya91d12.r3 Stratagene placenta (#937225) Homo sapiens
cDNA clone
          IMAGE:69047 5' similar to similar to gb:M58525 CATECHOL
          O-METHYLTRANSFERASE, MEMBRANE-BOUND FORM (HUMAN)
          Length = 217

 Score =  120 bits (300), Expect = 2e-26
 Identities = 57/69 (82%), Positives = 58/69 (83%)
 Frame = +1

Query: 27 RHWGWGLCLIGWNEFILQPIHNLLMGDTKEQRILNHVLQHAEPGNAQSVLEAIDTYCEQK 86
          RH    LCLIGWNEFILQPIHNLLMGDTKEQRILNHVLQH  P N QSVLEAI+TY EQ 
Sbjct: 10 RHXX*XLCLIGWNEFILQPIHNLLMGDTKEQRILNHVLQHXXPXNXQSVLEAINTYXEQX 189

Query: 87 EWAMNVGDK 95
          EW MNVGDK
Sbjct: 190EWXMNVGDK 216
         ^

Adding a space after 190 removed the error.

For those interested the error was

Use of uninitialized value in concatenation (.) at
/home/mxw02/bioperl_latest/lib/site_perl/5.6.0/Bio/SearchIO/blast.pm line
629, <GEN3> line 9401.

Maybe this is known, maybe not, must be rare?


-Mat