Post by Agu on Dec 8th, 2010 at 5:58pm
Hi!
I found a funny bug. UGENE is not compatible with itself :o.
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?)
https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=Exported_UGENE.msf (1 KB | ) https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=corrected.msf (1 KB | ) https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=Exported_seaview.msf (1 KB | )
I found a funny bug. UGENE is not compatible with itself :o.
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?)
https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=Exported_UGENE.msf (1 KB | ) https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=corrected.msf (1 KB | ) https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=Exported_seaview.msf (1 KB | )