[Biopython-dev] [Bug 1411] New: t_coffee *.aln reading

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

http://bugzilla.bioperl.org/show_bug.cgi?id=1411

           Summary: t_coffee *.aln reading
           Product: Biopython
           Version: Not Applicable
          Platform: All
               URL: http://cvs.biopython.org/cgi-
                    bin/viewcvs/viewcvs.cgi/biopython/Bio/Clustalw/clustal_f
                    ormat.py?rev=1.5&cvsroot=biopython&content-
                    type=text/vnd.viewcvs-markup
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: ktdiedrich at yahoo.com


The Bio.Clustalw.clustal_format file cannot read t_coffee
alignments which are the same a Clustalw alignments except 
for the header. 

By making the regular expression for the header more general 
both can be read.

A diff -c that makes Bio.Clustalw.clustal_format work for both is:
*** clustal_format.py   Sun Mar 16 11:09:29 2003
--- clustal_format.py.orig      Sun Mar 16 10:12:50 2003
***************
*** 24,30 ****

  header = Martel.Group("header",
                       Martel.Str("CLUSTAL ") +
!                      Martel.Re(".+") +
                       Martel.MaxRepeat(Martel.AnyEol(), 0, 3))

  seq_id = Martel.Group("seq_id",
--- 24,33 ----

  header = Martel.Group("header",
                       Martel.Str("CLUSTAL ") +
!                      Martel.Re("[X|W]") +
!                      Martel.Re("[ (]+") +
!                      version +
!                      Martel.Str(") multiple sequence alignment") +
                       Martel.MaxRepeat(Martel.AnyEol(), 0, 3))

  seq_id = Martel.Group("seq_id",



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