UGENE Forum - Suggestion for minor change in how UGENE reads Clustal alignments


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Suggestion for minor change in how UGENE reads Clustal alignments (Read 5837 times)

Apr 3^rd, 2009 at 12:56am

David Spencer Offline
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Hi,

We just discovered (and I verified by going through the source code) that when UGENE imports a clustal 'aln' file it checks the first line for the string "CLUSTAL W". Unfortunately 'clustalx' (the gui front end to 'clustalw') uses the identifier 'CLUSTAL X' here so UGENE imports it but the data gets messed up when it is displayed.
I assume that UGENE could look for simply 'CLUSTAL' in 'aln' files because I assume that either few people use 'clustalv' anymore, or maybe the file format is the same for it anyway. The change I am suggesting is pretty basic and I will probably edit the source and rebuild for my linux and Mac OS X environments but for this student's Window's machine ( Tongue

) I don't have a compiler and have no interest in getting one.

Thanks (nice program!)

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Reply #1 - Apr 3^rd, 2009 at 12:40pm

Mikhail Fursov Offline
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Posts: 162

Hi David!
Thanks for report.

We will include the fix to v1.4.2.

I attached the diff: it changes 2 places in ClustalFormat.cpp: a function with format detection by a file header and format reading function.

Actually I think we need to keep a header in model and reuse it when alignment file is saved. This feature is not in the diff, but it will also be added to the next minor release.

clustal.diff (0 KB | )

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UGENE team

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