centroidedPeaks() throws an IndexError with some mzML files

[ajmazurie]

I've been using pymzML extensively over the last few months without problems. Recently I have been processing mzML files converted from data collected on an older machine (Agilent 6430, from 2009) and got the following when attempting to extract centroided peaks:

Traceback (most recent call last):
  File "../../../tools/rtms-extract-masses", line 182, in <module>
    for mz, intensity in spectrum.centroidedPeaks:
  File "/Users/ajmazurie/.pyenv/versions/2.7.6/lib/python2.7/site-packages/pymzml/spec.py", line 420, in centroidedPeaks
    self._centroidedPeaks = self._centroid_peaks()
  File "/Users/ajmazurie/.pyenv/versions/2.7.6/lib/python2.7/site-packages/pymzml/spec.py", line 474, in _centroid_peaks
    x3  = mz_array[pos+7]
IndexError: tuple index out of range

The same code works flawlessly with data obtained from a more recent machine (e.g., Agilent 6520). Is there anything that could be done to fix this issue?

Best, Aurelien

[fu]

Fixed this error. Thanks for the feedback!

[ajmazurie]

Ouch. It seems that I get a similar error in the same place:

Traceback (most recent call last):
  File "/Volumes/Magenta/workspace/BrianBothner_FlowSpectrometry/Runs/tools/rtms-extract-masses", line 200, in <module>
    for mz, intensity in spectrum.centroidedPeaks:
  File "/Users/ajmazurie/.pyenv/versions/2.7.6/lib/python2.7/site-packages/pymzml/spec.py", line 428, in centroidedPeaks
    self._centroidedPeaks = self._centroid_peaks()
  File "/Users/ajmazurie/.pyenv/versions/2.7.6/lib/python2.7/site-packages/pymzml/spec.py", line 490, in _centroid_peaks
    x3  = mz_array[ upper_pos ]
IndexError: tuple index out of range

[fu]

Hmm worked with me. I'll check if I have commit everything:) ups otherwise

Cheers

C

On 24.05.2014, at 07:35, Aurélien Mazurie, Ph.D. notifications@github.com wrote:

Ouch. It seems that I get a similar error in the same place:

Traceback (most recent call last): File "/Volumes/Magenta/workspace/BrianBothner_FlowSpectrometry/Runs/tools/rtms-extract-masses", line 200, in for mz, intensity in spectrum.centroidedPeaks: File "/Users/ajmazurie/.pyenv/versions/2.7.6/lib/python2.7/site-packages/pymzml/spec.py", line 428, in centroidedPeaks self._centroidedPeaks = self._centroid_peaks() File "/Users/ajmazurie/.pyenv/versions/2.7.6/lib/python2.7/site-packages/pymzml/spec.py", line 490, in _centroid_peaks x3 = mz_array[ upper_pos ] IndexError: tuple index out of range — Reply to this email directly or view it on GitHub.

[fu]

Hmm,

Is that the same mzml? If not can you mail/post me the file?

Cheers C

On 24.05.2014, at 07:35, Aurélien Mazurie, Ph.D. notifications@github.com wrote:

Ouch. It seems that I get a similar error in the same place:

Traceback (most recent call last): File "/Volumes/Magenta/workspace/BrianBothner_FlowSpectrometry/Runs/tools/rtms-extract-masses", line 200, in for mz, intensity in spectrum.centroidedPeaks: File "/Users/ajmazurie/.pyenv/versions/2.7.6/lib/python2.7/site-packages/pymzml/spec.py", line 428, in centroidedPeaks self._centroidedPeaks = self._centroid_peaks() File "/Users/ajmazurie/.pyenv/versions/2.7.6/lib/python2.7/site-packages/pymzml/spec.py", line 490, in _centroid_peaks x3 = mz_array[ upper_pos ] IndexError: tuple index out of range — Reply to this email directly or view it on GitHub.

[ajmazurie]

No, it's a different .mzML file. I'll send it to you by email today. Aurélien

[fu]

Hi Aurélien,

I am in a conference right now, but I'll be back @ Friday.

Let me get back to you then, ok?

Cheers,

.c

On 03.06.2014, at 21:19, Aurélien Mazurie, Ph.D. notifications@github.com wrote:

No, it's a different .mzML file. I'll send it to you by email today. Aurélien

— Reply to this email directly or view it on GitHub.

[fu]

Fixed it now :) Thanks for the feedback!

[ajmazurie]

Thanks! It appears to work perfectly now. Aurélien