[Bioperl-l] allowgaps parameter in Bio::SearchIO
Daniel Lang
Daniel.Lang at biologie.uni-freiburg.de
Fri Oct 31 08:54:24 EST 2003
Hi,
I´m getting wrong values for the "allowgaps" parameter while parsing
NCBI-like BLAST results:
The parser does not detect if a the report was generated with -g F
switch(ungapped) and the allowgaps values is "yes", when it should be
"no"...
I guess the parameter is based on the occurence of "Gapped" after the
"Lambda"-part, right?
Here is an example BLAST output snipplet(-g F):
Searching..................................................done
***** No hits found ******
Database: ppp_orfpep
Posted date: Sep 18, 2003 6:31 AM
Number of letters in database: 2,367,445
Number of sequences in database: 14,583
Lambda K H
0.318 0.135 0.401
Matrix: BLOSUM62
Number of Hits to DB: 378,425
Or did I missinterpret the parameter?
Thanks ind advance,
Daniel:)
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