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POConverting values of named tuples from strings to integers
 

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  1. POConverting values of named tuples from strings to integers
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    <p>I'm creating a script to read a csv file into a set of named tuples from their column headers. I will then use these namedtuples to pull out rows of data which meet certain criteria.</p> <p>I've worked out the input (shown below), but am having issues with filtering the data before outputting it to another file.</p> <pre><code>import csv from collections import namedtuple with open('test_data.csv') as f: f_csv = csv.reader(f) #read using csv.reader() Base = namedtuple('Base', next(f_csv)) #create namedtuple keys from header row for r in f_csv: #for each row in the file row = Base(*r) # Process row print(row) #print data </code></pre> <p>The contents of my input file are as follows:</p> <pre><code>Locus Total_Depth Average_Depth_sample Depth_for_17 chr1:6484996 1030 1030 1030 chr1:6484997 14 14 14 chr1:6484998 0 0 0 </code></pre> <p>And they are printed from my code as follow:</p> <blockquote> <p>Base(Locus='chr1:6484996', Total_Depth='1030', Average_Depth_sample='1030', Depth_for_17='1030') Base(Locus='chr1:6484997', Total_Depth='14', Average_Depth_sample='14', Depth_for_17='14') Base(Locus='chr1:6484998', Total_Depth='0', Average_Depth_sample='0', Depth_for_17='0')</p> </blockquote> <p>I want to be able to pull out only the records with a Total_Depth greater than 15.</p> <p>Intuitively I tried the following function:</p> <pre><code>if Base.Total_Depth &gt;= 15 : print row </code></pre> <p>However this only prints the final row of data (from the above output table). I think the problem is twofold. As far as I can tell I'm not storing my named tuples anywhere for them to be referenced later. And secondly the numbers are being read in string format rather than as integers.</p> <p>Firstly can someone correct me if I need to store my namedtuples somewhere.</p> <p>And secondly how do I convert the string values to integers? Or is this not possible because namedtuples are immutable.</p> <p>Thanks!</p> <p>I <a href="https://stackoverflow.com/questions/17238567/returning-a-row-from-a-csv-if-specified-value-within-the-row-matches-condition">previously asked a similar question</a> with respect to dictionaries, but now would like to use namedtuples instead. :)</p>
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