[Bioperl-guts-l] [Bug 2576] SearchIO is ignoring an excellent match

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2576





------- Comment #6 from cjfields at bioperl.org  2008-08-28 18:07 EST -------
The hit description line:

>gnl|ti|69081059 19866918836292

The last two integers matched the regex for the hit table:

$descline =~ /(?<!cor)          # negative lookahead
(\d*\.?(?:[\+\-eE]+)?\d+)       # number (float or scientific notation)
\s+                             # space
(\d*\.?(?:[\+\-eE]+)?\d+)       # number (float or scientific notation)
\s*$/xms

I could add a check for a space prior to the first number (which would directly
fix your specific problem).  The specific fix I added in just checks for an
empty line after the hit table and moves on to check for possible it data and
alignments.

Related to the problem you saw, there is a sanity check later on down the line
which compares the hit table name and alignment header name (if present) in the
alignment and skips them if present.  The remaining hit table data make up
minimal hit objects.


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