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POHow to copy an object without referencing to it?
 

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  1. POHow to copy an object without referencing to it?
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    <p>I'm not sure if my title is correct for what I'm looking for, but I think that the referencing is the problem.</p> <p>I have a Reader object through which I can loop:</p> <pre><code>msrun = pymzml.run.Reader(mzmlFile) for feature in msrun: print feature['id'] </code></pre> <p>With this code I get the id's, starting at 1, of all the features in msrun. However, I need to loop through the code first and get all the keys that I want and put them in a list, like this:</p> <pre><code>def getKeys(msrun, excludeList): spectrumKeys = [] done = False for spectrum in msrun: if done: break if spectrum['ms level'] == 2: for key in spectrum: if key not in excludeList and not key.startswith('MS:'): done = True spectrumKeys.append(key) spectrumKeys.extend(spectrum['precursors'][0].keys()) precursorKeys = spectrum['precursors'][0].keys() break return spectrumKeys, precursorKeys </code></pre> <p>However, if I would run this code:</p> <pre><code>msrun = pymzml.run.Reader(mzmlFile) specKeys, precursKeys = getKeys(msrun, ['title','name']) for feature in msrun: print feature['id'] </code></pre> <p>it starts of at the id that hasn't been in the loop in getKeys() (it starts at 11 instead of 1). So I guess pymzml.run.Reader() works like a generator object. So I tried copying the object. First I tried</p> <pre><code>copyMsrun = msrun specKeys, precursKeys = getKeys(copyMsrun, ['title','name']) </code></pre> <p>But this gives the same problem, if I understood correctly because doing copyMsrun = msrun makes them point to the same thing.</p> <p>Then I tried</p> <pre><code>import copy copyMsrun = copy.copy(msrun) </code></pre> <p>But I still had the same problem. I used copy.copy instead of copy.deepcopy because I don't think that the Reader objects contains other objects, and when I try deepcopy I get </p> <pre><code>TypeError: object.__new__(generator) is not safe, use generator.__new__(). </code></pre> <p>So how <strong>do</strong> I copy an object so that looping through one doesn't affect the other? Should I just do</p> <pre><code>msrun = pymzml.run.Reader(mzmlFile) copyMsrun = pymzml.run.Reader(mzmlFile) </code></pre> <p>?</p> <hr> <p>Edit: On Ade YU's comment, I tried that too but when I do </p> <pre><code>spectrumList = [] for spectrum in msrun: print spectrum['id'] spectrumList.append(spectrum) for spectrum in spectrumList: print spectrum['id'] </code></pre> <p>The first print gives me 1-10, but the second print give me ten times 10 </p>
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    1. COYou may pick as much info as you need in the first loop and store them in some basic data structure, which you can easily manipulate.
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      1. USAde YU
 

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