[Chimera-users] Fwd: single-sequence FASTA file does not open

Lucas J. Thode ThodeL74 at ops.org
Thu Oct 12 06:34:11 PDT 2006

Oops, sorry about double-posting this, but I forgot to mention that I am
not on the list, so remember to CC me.
----- Original Message -----

In Chimera beta 1 build 2199 on Windows XP Professional SP2, I cannot open
a FASTA file that contains a single sequence.  (The file in question is
attached and looks to be a valid FASTA file according to the documentation
I have read on the FASTA format.)  What should I do about this issue?

Error log:
Opening F:\H Biotech Engineering\cftr.fasta
Error reading F:\H Biotech Engineering\cftr.fasta:
IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech
Engineering\cftr.fasta'; check your alignment file for errors
(see reply log for Python traceback info)
Traceback (most recent call last):
  File "C:\Program Files\Chimera\share\__main__.py", line 59, in ?
    value = chimeraInit.init(sys.argv)
  File "C:\Program Files\Chimera\share\chimeraInit.py", line 308, in init
  File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2757, in
  File "C:\Program Files\Chimera\bin\Lib\lib-tk\Tkinter.py", line 965, in
  File "C:\Program
Files\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line
1747, in __call__
    return apply(self.func, args)
  File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 229,
in <lambda>
  File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 470,
in OK
  File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 160, in
    openPath(path, ftype)
  File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 258, in
    mols = chimera.openModels.open(path, type=ftype)
  File "C:\Program Files\Chimera\share\chimera\__init__.py", line 1086, in
    models = func(filename, *args, **kw)
  File "C:\Program
Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 33, in
    lambda fn, e=emo, ft=fileType: e.open(fn, ft),
  File "C:\Program
Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 25, in open
    self.module('MAViewer').MAViewer(fileName, fileType)
  File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py", line
59, in __init__
    seqs, fileAttrs, fileMarkups = self.readFile(
  File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py", line
761, in readFile
    seqs, fileAttrs, fileMarkups = parseFile(fileName, fileType)
  File "C:\Program Files\Chimera\share\MultAlignViewer\parse.py", line
100, in parseFile
    raise IOError("Only one sequence found in %s file"
IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech
Engineering\cftr.fasta'; check your alignment file for errors
Done opening F:\H Biotech Engineering\cftr.fasta

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