[BioRuby] Parsing MSF alignment file

[Fredrik Johansson]

Yes, that's what happened. A regular expression matched all the way to 
the last occurrence of two dots at the end of a line.
> Thank you very much.  Do you mean that Bio::GCG::Msf fails to
> parse an alignment that contain two contiguous gaps (..) in the
> end of a line?  This is a bug, and the patch will soon be
> applied to the git repository. 
>
>   
>> $ diff msf.rb.old msf.rb.new
>>     
>
> In the next time, please use "diff -u" (unified context format).
>
>   
Ok, I'll attach the output of diff -u here:

--- /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/gcg/msf.rb.old    
2009-04-13 11:32:53.000000000 +0900
+++ /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/gcg/msf.rb    
2009-04-13 13:36:26.000000000 +0900
@@ -30,11 +30,12 @@
       # Creates a new Msf object.
       def initialize(str)
         str = str.sub(/\A[\r\n]+/, '')
-        if /^\!\![A-Z]+\_MULTIPLE\_ALIGNMNENT/ =~ str[/.*/] then
-          @heading = str[/.*/] # '!!NA_MULTIPLE_ALIGNMENT 1.0' or like this
-          str.sub!(/.*/, '')
+        preamble, at data = str.split(/^\/\/$/)
+        if /^\!\![A-Z]+\_MULTIPLE\_ALIGNMNENT/ =~ preamble[/.*/] then
+          @heading = preamble[/.*/] # '!!NA_MULTIPLE_ALIGNMENT 1.0' or 
like this
+          preamble.sub!(/.*/, '')
         end
-        str.sub!(/.*\.\.$/m, '')
+        preamble.sub!(/.*\.\.$/m, '')
         @description = $&.to_s.sub(/^.*\.\.$/, '').to_s
         d = $&.to_s
         if m = 
/(.+)\s+MSF\:\s+(\d+)\s+Type\:\s+(\w)\s+(.+)\s+(Comp)?Check\:\s+(\d+)/.match(d) 
then
@@ -45,10 +46,8 @@
           @checksum = (m[6] ? m[6].to_i : nil)
         end
 
-        str.sub!(/.*\/\/$/m, '')
-        a = $&.to_s.split(/^/)
         @seq_info = []
-        a.each do |x|
+        preamble.split(/^/).each do |x|
           if /Name\: / =~ x then
             s = {}
             x.scan(/(\S+)\: +(\S*)/) { |y| s[$1] = $2 }
@@ -56,7 +55,6 @@
           end
         end
 
-        @data = str
         @description.sub!(/\A(\r\n|\r|\n)/, '')
         @align = nil
       end