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<li><a class="reference internal" href="#">Reading and Writing files in Pure Python</a><ul>
<li><a class="reference internal" href="#reading">Reading</a></li>
<li><a class="reference internal" href="#writing">Writing</a></li>
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<div class="section" id="reading-and-writing-files-in-pure-python">
<h1>Reading and Writing files in Pure Python<a class="headerlink" href="#reading-and-writing-files-in-pure-python" title="Permalink to this headline">¶</a></h1>
<div class="section" id="reading">
<h2>Reading<a class="headerlink" href="#reading" title="Permalink to this headline">¶</a></h2>
<p>We have already talked about <a class="reference internal" href="../python/types.html#python-built-in-types-and-operations"><em>Python Built-in Types and Operations</em></a>, but
there are more types that we did not speak about. One of these is the
<tt class="docutils literal"><span class="pre">file()</span></tt> object which can be used to read or write files.</p>
<p>Let’s start off by downloading <a class="reference download internal" href="../_downloads/data.txt"><tt class="xref download docutils literal"><span class="pre">this</span></tt></a> data file, then launching IPython the directory where you have the file:</p>
<div class="highlight-python"><pre>$ ipython -pylab</pre>
</div>
<p>If you have trouble downloading the file, then start up IPython (<tt class="docutils literal"><span class="pre">ipython</span> <span class="pre">-pylab</span></tt>) and enter:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">urllib2</span>
<span class="n">url</span> <span class="o">=</span> <span class="s">'http://python4astronomers.github.com/_downloads/data.txt'</span>
<span class="nb">open</span><span class="p">(</span><span class="s">'data.txt'</span><span class="p">,</span> <span class="s">'wb'</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">urllib2</span><span class="o">.</span><span class="n">urlopen</span><span class="p">(</span><span class="n">url</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
<span class="n">ls</span>
</pre></div>
</div>
<p>Now let’s try and get the contents of the file into IPython. We start off by creating a file object:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">'data.txt'</span><span class="p">,</span> <span class="s">'r'</span><span class="p">)</span>
</pre></div>
</div>
<p>The <tt class="docutils literal"><span class="pre">'r'</span></tt> means that the file should be opened in <em>read</em> mode (i.e. you will get an error if the file does not exist). Now, simply type:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
</pre></div>
</div>
<p>and you will see something like this:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
<span class="go">'RAJ DEJ Jmag e_Jmag\n2000 (deg) 2000</span>
<span class="go">(deg) 2MASS (mag) (mag) \n---------- ----------</span>
<span class="go">----------------- ------ ------\n010.684737 +41.269035 00424433+4116085</span>
<span class="go">9.453 0.052\n010.683469 +41.268585 00424403+4116069 9.321</span>
<span class="go">0.022\n010.685657 +41.269550 00424455+4116103 10.773 0.069\n010.686026</span>
<span class="go">+41.269226 00424464+4116092 9.299 0.063\n010.683465 +41.269676</span>
<span class="go">00424403+4116108 11.507 0.056\n010.686015 +41.269630</span>
<span class="go">00424464+4116106 9.399 0.045\n010.685270 +41.267124</span>
<span class="go">00424446+4116016 12.070 0.035\n'</span>
</pre></div>
</div>
<p>The data file has been read in as a single string. Let’s try that again:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
<span class="go">''</span>
</pre></div>
</div>
<p>What’s happened? We read the file, and the file ‘pointer’ is now sitting at the end of the file, and there is nothing left to read. Let’s now try and do something more useful, and capture the contents of the file in a string:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">'data.txt'</span><span class="p">,</span> <span class="s">'r'</span><span class="p">)</span> <span class="c"># We need to re-open the file</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
</pre></div>
</div>
<p>Now <tt class="docutils literal"><span class="pre">data</span></tt> contains a string:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="nb">type</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="go"><type 'str'></span>
</pre></div>
</div>
<p>But what we’d really like to do is read the file line by line. There are several ways to do this, the simplest of which is to use a <tt class="docutils literal"><span class="pre">for</span></tt> loop in the following way:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">'data.txt'</span><span class="p">,</span> <span class="s">'r'</span><span class="p">)</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">f</span><span class="p">:</span>
<span class="k">print</span> <span class="nb">repr</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
</pre></div>
</div>
<p>Notice the indent before <tt class="docutils literal"><span class="pre">print</span></tt>, which is necessary to indicate that we are inside the loop (there is no <tt class="docutils literal"><span class="pre">end</span> <span class="pre">for</span></tt> in Python). Note that we are using <tt class="docutils literal"><span class="pre">repr()</span></tt> to show any invisible characters (this will be useful in a minute). The output should now look something like this:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">f</span><span class="p">:</span>
<span class="go"> print repr(line)</span>
<span class="go">'RAJ DEJ Jmag e_Jmag\n'</span>
<span class="go">'2000 (deg) 2000 (deg) 2MASS (mag) (mag) \n'</span>
<span class="go">'---------- ---------- ----------------- ------ ------\n'</span>
<span class="go">'010.684737 +41.269035 00424433+4116085 9.453 0.052\n'</span>
<span class="go">'010.683469 +41.268585 00424403+4116069 9.321 0.022\n'</span>
<span class="go">'010.685657 +41.269550 00424455+4116103 10.773 0.069\n'</span>
<span class="go">'010.686026 +41.269226 00424464+4116092 9.299 0.063\n'</span>
<span class="go">'010.683465 +41.269676 00424403+4116108 11.507 0.056\n'</span>
<span class="go">'010.686015 +41.269630 00424464+4116106 9.399 0.045\n'</span>
<span class="go">'010.685270 +41.267124 00424446+4116016 12.070 0.035\n'</span>
</pre></div>
</div>
<p>Each line is being returned as a string. Notice the <tt class="docutils literal"><span class="pre">\n</span></tt> at the end of each line - this is a line return character, which indicates the end of a line.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p>You may also come across the following way to read files line by
line:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">f</span><span class="o">.</span><span class="n">readlines</span><span class="p">():</span>
<span class="o">...</span>
</pre></div>
</div>
<p><tt class="docutils literal"><span class="pre">f.readlines()</span></tt> actually reads in the whole file and splits it
into a list of lines, so for large files this can be memory
intensive. Using:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">f</span><span class="p">:</span>
<span class="o">...</span>
</pre></div>
</div>
<p class="last">instead is more memory efficient because it only reads one line
at a time.</p>
</div>
<p>Now we’re reading in a file line by line, what would be really nice would be to get some values out of it. Let’s examine the last line in detail. If we just type <tt class="docutils literal"><span class="pre">line</span></tt> we should see the last line that was printed in the loop:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">line</span>
<span class="go">'010.685270 +41.267124 00424446+4116016 12.070 0.035\n'</span>
</pre></div>
</div>
<p>We can first get rid of the <tt class="docutils literal"><span class="pre">\n</span></tt> character with:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
<span class="gp">>>> </span><span class="n">line</span>
<span class="go">'010.685270 +41.267124 00424446+4116016 12.070 0.035'</span>
</pre></div>
</div>
<p>Next, we can use what we learned about strings and lists to do:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">columns</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
<span class="gp">>>> </span><span class="n">columns</span>
<span class="go">['010.685270', '+41.267124', '00424446+4116016', '12.070', '0.035']</span>
</pre></div>
</div>
<p>Finally, let’s say we care about the source name, and the J band magnitude. We can extract these with:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">name</span> <span class="o">=</span> <span class="n">columns</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="gp">>>> </span><span class="n">j</span> <span class="o">=</span> <span class="n">columns</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
<span class="gp">>>> </span><span class="n">name</span>
<span class="go">'00424446+4116016'</span>
<span class="gp">>>> </span><span class="n">j</span>
<span class="go">'12.070'</span>
</pre></div>
</div>
<p>Note that <tt class="docutils literal"><span class="pre">j</span></tt> is a string, but if we want a floating point number, we can instead do:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">j</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">columns</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span>
</pre></div>
</div>
<p>One last piece of information we need about files is how we can read a single line. This is done using:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">line</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
</pre></div>
</div>
<p>We can put all this together to write a little script to read the data from the file and display the columns we care about to the screen! Here is is:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="c"># Open file</span>
<span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">'data.txt'</span><span class="p">,</span> <span class="s">'r'</span><span class="p">)</span>
<span class="c"># Read and ignore header lines</span>
<span class="n">header1</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
<span class="n">header2</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
<span class="n">header3</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
<span class="c"># Loop over lines and extract variables of interest</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">f</span><span class="p">:</span>
<span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
<span class="n">columns</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
<span class="n">name</span> <span class="o">=</span> <span class="n">columns</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="n">j</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">columns</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span>
<span class="k">print</span> <span class="n">name</span><span class="p">,</span> <span class="n">j</span>
</pre></div>
</div>
<p>The output should look like this:</p>
<div class="highlight-python"><pre>00424433+4116085 9.453
00424403+4116069 9.321
00424455+4116103 10.773
00424464+4116092 9.299
00424403+4116108 11.507
00424464+4116106 9.399
00424446+4116016 12.07</pre>
</div>
<div class="admonition-exercise admonition ">
<p class="first admonition-title">Exercise</p>
<p>Try and see if you can understand what the following script is doing:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">'data.txt'</span><span class="p">,</span> <span class="s">'r'</span><span class="p">)</span>
<span class="n">header1</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
<span class="n">header2</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
<span class="n">header3</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
<span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">f</span><span class="p">:</span>
<span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
<span class="n">columns</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
<span class="n">source</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">source</span><span class="p">[</span><span class="s">'name'</span><span class="p">]</span> <span class="o">=</span> <span class="n">columns</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="n">source</span><span class="p">[</span><span class="s">'j'</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">columns</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span>
<span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
</pre></div>
</div>
<p class="last">After this script is run, how would you access the name and J-band magnitude of the third source?</p>
</div>
<p class="flip7">Click to Show/Hide Solution</p> <div class="panel7"><p>The following line creates an empty list to contain all the data:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
</pre></div>
</div>
<p>For each line, we are then creating an empty dictionary and populating it with variables we care about:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">source</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">source</span><span class="p">[</span><span class="s">'name'</span><span class="p">]</span> <span class="o">=</span> <span class="n">columns</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="n">source</span><span class="p">[</span><span class="s">'j'</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">columns</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span>
</pre></div>
</div>
<p>Finally, we append this source to the <tt class="docutils literal"><span class="pre">data</span></tt> list:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
</pre></div>
</div>
<p>Therefore, <tt class="docutils literal"><span class="pre">data</span></tt> is a list of dictionaries:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">data</span>
<span class="go">[{'j': 9.453, 'name': '00424433+4116085'},</span>
<span class="go"> {'j': 9.321, 'name': '00424403+4116069'},</span>
<span class="go"> {'j': 10.773, 'name': '00424455+4116103'},</span>
<span class="go"> {'j': 9.299, 'name': '00424464+4116092'},</span>
<span class="go"> {'j': 11.507, 'name': '00424403+4116108'},</span>
<span class="go"> {'j': 9.399, 'name': '00424464+4116106'},</span>
<span class="go"> {'j': 12.07, 'name': '00424446+4116016'}]</span>
</pre></div>
</div>
<p>You can access the dictionary for the third source with:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="go">{'j': 10.773, 'name': '00424455+4116103'}</span>
</pre></div>
</div>
<p>To get the name of this source, you can therefore do:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">data</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="s">'name'</span><span class="p">]</span>
<span class="go">'00424455+4116103'</span>
</pre></div>
</div>
</div></div>
<div class="section" id="writing">
<h2>Writing<a class="headerlink" href="#writing" title="Permalink to this headline">¶</a></h2>
<p>To open a file for writing, use:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">'data_new.txt'</span><span class="p">,</span> <span class="s">'wb'</span><span class="p">)</span>
</pre></div>
</div>
<p>Then simply use <tt class="docutils literal"><span class="pre">f.write()</span></tt> to write any content to the file, for example:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Hello, World!</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
</pre></div>
</div>
<p>If you want to write multiple lines, you can either give a list of strings to the <tt class="docutils literal"><span class="pre">writelines()</span></tt> method:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">f</span><span class="o">.</span><span class="n">writelines</span><span class="p">([</span><span class="s">'spam</span><span class="se">\n</span><span class="s">'</span><span class="p">,</span> <span class="s">'egg</span><span class="se">\n</span><span class="s">'</span><span class="p">,</span> <span class="s">'spam</span><span class="se">\n</span><span class="s">'</span><span class="p">])</span>
</pre></div>
</div>
<p>or you can write them as a single string:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'spam</span><span class="se">\n</span><span class="s">egg</span><span class="se">\n</span><span class="s">spam'</span><span class="p">)</span>
</pre></div>
</div>
<p>To close a file, simply use:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
</pre></div>
</div>
<p>(this also applies to reading files)</p>
<div class="admonition-exercise admonition ">
<p class="first admonition-title">Exercise</p>
<p>Let’s try combining reading and writing. Using at most seven lines, write a script which will read in <tt class="docutils literal"><span class="pre">data.txt</span></tt>, replace any spaces with periods (<tt class="docutils literal"><span class="pre">.</span></tt>), and write the result out to a file called <tt class="docutils literal"><span class="pre">data_new.txt</span></tt>.</p>
<p class="last">Can you do it in a single line? (you can ignore closing the file)</p>
</div>
<p class="flip6">Click to Show/Hide Solution</p> <div class="panel6"><p>Here is a possible solution:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">f1</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">'data.txt'</span><span class="p">,</span> <span class="s">'r'</span><span class="p">)</span>
<span class="n">content</span> <span class="o">=</span> <span class="n">f1</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
<span class="n">f1</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="n">content</span> <span class="o">=</span> <span class="n">content</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">' '</span><span class="p">,</span><span class="s">'.'</span><span class="p">)</span>
<span class="n">f2</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">'data_new.txt'</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span>
<span class="n">f2</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">content</span><span class="p">)</span>
<span class="n">f2</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
</pre></div>
</div>
<p>And a possible one-liner!:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="nb">open</span><span class="p">(</span><span class="s">'data_new.txt'</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s">'data.txt'</span><span class="p">,</span> <span class="s">'r'</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">' '</span><span class="p">,</span> <span class="s">'.'</span><span class="p">))</span>
</pre></div>
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