[BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb,1.25,1.26

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory dev.open-bio.org:/tmp/cvs-serv9861/lib/bio/appl/blast

Modified Files:
	format0.rb 
Log Message:
* Bug fixes reported by Shuji Shigenobu.
  * Failed to parse query length for long query (>= 10000 letters)
    because comma is inserted for digit separator by blastall.
  * Failed to parse e-value for some BLASTX results


Index: format0.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** format0.rb	27 Dec 2007 17:28:57 -0000	1.25
--- format0.rb	12 Feb 2008 02:13:31 -0000	1.26
***************
*** 265,270 ****
                  q << sc.scan(/.*/)
                  sc.skip(/\s*^ ?/)
!               end until !sc.rest or r = sc.skip(/ *\( *(\d+) *letters *\)\s*\z/)
!               @query_len = sc[1].to_i if r
                @query_def = q.join(' ')
              end
--- 265,270 ----
                  q << sc.scan(/.*/)
                  sc.skip(/\s*^ ?/)
!               end until !sc.rest or r = sc.skip(/ *\( *([\,\d]+) *letters *\)\s*\z/)
!               @query_len = sc[1].delete(',').to_i if r
                @query_def = q.join(' ')
              end
***************
*** 969,973 ****
                while sc.rest?
                  sc.skip(/\s*/)
!                 if sc.skip(/Expect(?:\(\d\))? *\= *([e\-\.\d]+)/) then
                    ev = sc[1].to_s
                    ev = '1' + ev if ev[0] == ?e
--- 969,973 ----
                while sc.rest?
                  sc.skip(/\s*/)
!                 if sc.skip(/Expect(?:\(\d+\))? *\= *([e\-\.\d]+)/) then
                    ev = sc[1].to_s
                    ev = '1' + ev if ev[0] == ?e