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copied!<h2>Answer</h2> <p>Let's break it down into pieces. Especially the pieces you got wrong. :)</p> <hr> <h3>Assignment</h3> <blockquote> <pre><code>outfile=ReadsAgain.txt </code></pre> </blockquote> <p>It should come to little surprise that you need to put quotes around strings. On the other hand, you have the luxury of putting spaces around the <code>=</code> for readability.</p> <pre><code>outfilename = "ReadsAgain.txt" </code></pre> <hr> <h3>Variable expansion → <a href="http://docs.python.org/library/stdtypes.html#str.format" rel="nofollow noreferrer"><code>str.format</code></a> (or, the <a href="http://docs.python.org/library/stdtypes.html#string-formatting-operations" rel="nofollow noreferrer"><code>%</code></a> operation)</h3> <blockquote> <pre><code>python reads.py <snip/> -q$queries <snip/> </code></pre> </blockquote> <p>So you know how to do the redirection already, but how do you do the variable expansion? You can use <a href="http://docs.python.org/library/stdtypes.html#str.format" rel="nofollow noreferrer">the <code>format</code> method</a> (v2.6+):</p> <pre><code>command = "python reads.py -r1 -pquery1.sql -q{0} -shotelspec -k6 -a5".format(queries) </code></pre> <p>You can alternatively use <a href="http://docs.python.org/library/stdtypes.html#string-formatting-operations" rel="nofollow noreferrer">the <code>%</code> operator</a>:</p> <pre><code>#since queries is a number, use %d as a placeholder command = "python reads.py -r1 -pquery1.sql -q%d -shotelspec -k6 -a5" % queries </code></pre> <hr> <h3>C-style loop → <a href="http://docs.python.org/tutorial/controlflow.html#for-statements" rel="nofollow noreferrer">Object-oriented-style loop</a></h3> <blockquote> <pre><code>for ((r = 1; r < ($runs + 1); r++)) do done </code></pre> </blockquote> <p>Looping in Python is different from C-style iteration. What happens in Python is you iterate over an iterable object, like for example a list. Here, you are trying to do something <code>runs</code> times, so you would do this:</p> <pre><code>for r in range(runs): #loop body here </code></pre> <p><code>range(runs)</code> is equivalent to <code>[0,1,...,runs-1]</code>, a list of <code>runs = 5</code> integer elements. So you'll be repeating the body <code>runs</code> times. At every cicle, <code>r</code> is assigned the next item of the list. This is thus completely equivalent to what you are doing in Bash.</p> <p>If you're feeling daring, use <a href="http://docs.python.org/library/functions.html#xrange" rel="nofollow noreferrer"><code>xrange</code></a> instead. It's completely equivalent but uses more advanced language features (so it is harder to explain in layman's terms) but consumes less resources.</p> <hr> <h3>Output redirection → <a href="http://docs.python.org/library/subprocess.html?highlight=subprocess#using-the-subprocess-module" rel="nofollow noreferrer">the <code>subprocess</code> module</a></h3> <p>The "tougher" part, if you will: executing a program and getting its output. <a href="http://www.google.com/search?q=how+to+get+the+output+of+a+program+python" rel="nofollow noreferrer">Google to the rescue!</a> Obviously, the top hit is a stackoverflow question: <a href="https://stackoverflow.com/questions/748028/how-to-get-output-of-exe-in-python-script">this one</a>. You can hide all the complexity behind it with a simple function:</p> <pre><code>import subprocess, shlex def get_output_of(command): args = shlex.split(command) return subprocess.Popen(args, stdout=subprocess.PIPE).communicate()[0] # this only returns stdout </code></pre> <p>So:</p> <blockquote> <pre><code>python reads.py -r1 -pquery1.sql -q$queries -shotelspec -k6 -a5 >> $outfile </code></pre> </blockquote> <p>becomes:</p> <pre><code>command = "python reads.py -r1 -pquery1.sql -q%s -shotelspec -k6 -a5" % queries read_result = get_output_of(command) </code></pre> <hr> <h3>Don't over-<code>subprocess</code>, batteries are included</h3> <p>Optionally, consider that you can get pretty much the same output of <code>date</code> with the following:</p> <pre><code>import time time_now = time.strftime("%c", time.localtime()) # Sat May 15 15:42:47 2010 </code></pre> <p>(Note the absence of the time zone information. This should be the subject of <a href="https://stackoverflow.com/questions/ask">another question</a>, if it is important to you.)</p> <hr> <h3>How your program should look like</h3> <p>The final result should then look like this:</p> <pre><code>import subprocess, shlex, time def get_output_of(command): #... body of get_output_of #... more functions ... if __name__ = "__main__": #only execute the following if you are calling this .py file directly, #and not, say, importing it #... initialization ... with file("outputfile.txt", "a") as output_file: #alternative way to open files, v2.5+ #... write date and other stuff ... for r in range(runs): #... loop body here ... </code></pre> <hr> <h2>Post scriptum</h2> <p>That must look pretty horrible when compared to the relatively simple and short Bash script, right? Python is not a specialized language: it aims to do everything reasonably well, but isn't built directly for running programs and getting the output of those.</p> <p>Still, you wouldn't <em>normally</em> write a database engine in Bash, right? It's different tools for different jobs. Here, unless you're planning to make some changes that would be non-trivial to write with that language, [Ba]sh was definitely the right choice.</p>

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