UGENE Forum - MSF Problem


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MSF Problem (Read 5015 times)

Dec 8^th, 2010 at 5:58pm

Agu Offline
Junior Member
(Argentinian)

Gender:
Posts: 63

Hi!
I found a funny bug. UGENE is not compatible with itself Shocked

.
After exporting an alignment as MSF, I can't open it with UGENE, but I have no problems opening it with other programs. Re-exporting with one of them, makes the file again compatible with UGENE. The problem is solved if the names of the sequences are in uppercase and without spaces. So, it seems that the reading of the files is not flexible enough.
I noticed as well (although there is no problem with it) that the word PileUp is missing at the beginning and that the "Type" is always "P" (protein) in UGENE, while it should be "N" (nucleotide) in this case.
Find attached some files to check.

Exported UGENE.msf: alignment exported from UGENE, without modifications.
corrected.msf: same alignment, but manually modified to work in ugene.
Exported seaview.msf: Exported UGENE.msf opened by seview and re-exported, as model of msf format (UGENE can't open it).

Version 1.8.0 (BTW, do you have a date for the new one?)

Exported_UGENE.msf (1 KB | )

corrected.msf (1 KB | )

Exported_seaview.msf (1 KB | )

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Reply #1 - Dec 8^th, 2010 at 7:56pm

Mikhail Fursov Offline
YaBB Administrator

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Posts: 162

Thank you for the feedback!

The most of the MSF issues are fixed.

Minor issues left unfixed

1) UGENE still not able to open MSF files with spaces in sequence names
2) We do not write 'PileUp' header line. It's not always clear for us what to write there.

The next release is expected next week (Monday or Tuesday)

---
UGENE team

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Reply #2 - Dec 9^th, 2010 at 4:24pm

Agu Offline
Junior Member
(Argentinian)

Gender:
Posts: 63

Thanks for the quick reply.

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