Hi,

I'm getting the following error:

File "/usr/local/sbin/chimera/share/MultAlignViewer/SeqCanvas.py", line 1057 self.rulerTexts.append(text) ^ SyntaxError: invalid syntax

I had to modify the file manually since the line numbers didn't match. This is my diff (unified format):

--- SeqCanvas.py 2005-08-09 14:45:57.000000000 -0500 +++ SeqCanvas.py.bak 2005-08-09 14:34:01.000000000 -0500 @@ -1045,19 +1045,13 @@ x = self.labelWidth + self.letterGaps[0] + self.fontPixels[0]/2 y = self.topY + self.fontPixels[1] + self.letterGaps[1]

- end = min(self.seqOffset + self.lineWidth, len (self.seqs[0])) - for chunkStart in range(self.seqOffset, end, 10): - seq1index = self.seqs[0].gapped2ungapped (chunkStart) - if seq1index is None: - dispText = "?" - else: - dispText = str(seq1index+1) - text = self.mainCanvas.create_text(x, y, anchor='s', - font=self.font, text="%s" % (dispText)) - self.rulerTexts.append(text) - x += self.chunkGap + 10 * (self.fontPixels[0] - + self.letterGaps[0]) - + end = min(self.seqOffset + self.lineWidth, len(self.seqs[0])) + for chunkStart in range(self.seqOffset, end, 10): + text = self.mainCanvas.create_text(x, y, anchor='s', + font=self.font, text="%d" % (chunkStart+1)) + self.rulerTexts.append(text) + x += self.chunkGap + 10 * (self.fontPixels[0] + +self.letterGaps[0]) if not rerule: self.bottomY += self.fontPixels[1] + self.letterGaps[1] self.bottomRulerY = self.bottomY

Thanks, Sabuj

Eric Pettersen wrote:

Hi Sabuj, I've appended a context diff for MAV's SeqCanvas.py file. It makes the ruler use the ungapped numbering of the first sequence. For positions where there is a gap in the first sequence it uses '?'. I think this is what you wanted, but let me know if I got that wrong. On another note, the new AL2CO conservation measures in the 1.2154 snapshot don't work on the Mac and possibly on Linux (depending on your execution path). If you want to get them to work, I've also appended a context diff for Conservation.py below and have also made the entire replacement file available at http:// www.cgl.ucsf.edu/home/pett/chimera/Conservation.py (which, on a Mac, you put in Chimera.app/Contents/Resources/share/MultAlignViewer [which you may have to use Terminal.app to access] and on Linux in <your install dir>/share/MultAlignViewer).

--Eric

On Aug 9, 2005, at 10:04 AM, Pattanayek, Sabuj wrote:

...

Hi all,

Is there a modification I can do to the multi-align viewer code so that "-" (gaps) characters are not counted in the alignment numbering (but are still displayed for alignment purposes) from a fasta file in the multi- align viewer? The numbering should correspond to the first sequence found in the fasta file (i.e. I don't care about the numbering due to gaps in the second, third, etc sequences).

Thanks, Sabuj Pattanayek

---

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*** SeqCanvas.py 6 Aug 2005 00:08:50 -0000 1.59 --- SeqCanvas.py 9 Aug 2005 17:57:45 -0000

---

*** 1056,1063 ****

            end = min(self.seqOffset + self.lineWidth, len 

(self.seqs[0])) for chunkStart in range(self.seqOffset, end, 10): text = self.mainCanvas.create_text(x, y, anchor='s', ! font=self.font, text="%d" % (chunkStart+1)) self.rulerTexts.append(text) x += self.chunkGap + 10 * (self.fontPixels[0] + self.letterGaps[0]) --- 1056,1068 ----

            end = min(self.seqOffset + self.lineWidth, len 

(self.seqs[0])) for chunkStart in range(self.seqOffset, end, 10):

•                   seq1index = self.seqs[0].gapped2ungapped 
  

(chunkStart)

•                   if seq1index is None:
  

•                           dispText = "?"
  

•                   else:
  

•                           dispText = str(seq1index+1)
                    text = self.mainCanvas.create_text(x, y,  
  

anchor='s', ! font=self.font, text="%s" % (dispText)) self.rulerTexts.append(text) x += self.chunkGap + 10 * (self.fontPixels[0] + self.letterGaps[0])

*** Conservation.py 3 Aug 2005 20:19:15 -0000 1.16 --- Conservation.py 9 Aug 2005 18:28:45 -0000

---

*** 56,62 **** tf = open(tfName, "w") save(tf, None, self.seqs, None) tf.close() ! command = "al2co -i %s -f %d -c %d -w %d -g %g" % (tfName, prefs[AL2CO_FREQ], prefs[AL2CO_CONS], prefs[AL2CO_WINDOW], prefs[AL2CO_GAP]) if prefs[AL2CO_CONS] == 2: --- 56,65 ---- tf = open(tfName, "w") save(tf, None, self.seqs, None) tf.close() ! import os, os.path ! chimeraRoot = os.environ.get("CHIMERA") ! command = os.path.join(chimeraRoot, 'bin', 'al2co') + \ ! " -i %s -f %d -c %d -w %d -g %g" % (tfName, prefs[AL2CO_FREQ], prefs[AL2CO_CONS], prefs[AL2CO_WINDOW], prefs[AL2CO_GAP]) if prefs[AL2CO_CONS] == 2: