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    <p>Does your version work? It looks like you only ever create one Peptide object. Also, what is the "if(row[5])" statement doing? In your example data there are always 5 elements. Also, mod_indeces is always supposed to be a list, correct? Because in your example output file mod_indeces isn't a list in the first peptide. Anyway, here is what I came up with in python:</p> <pre><code>import csv import json data = {} with open('proteins.csv','rb') as f: reader = csv.reader(f) for row in reader: name = row[0] sequence = row[1] mod_sequence = row[2] mod_indeces = map(int,row[3].split(', ')) spectral_count = int(row[4]) peptide = {'sequence':sequence,'mod_sequence':mod_sequence, 'mod_indeces':mod_indeces,'spectral_count':spectral_count} if name in data: data[name]['peptides'].append(peptide) else: data[name] = {'peptides':[peptide]} f.close() f = open('output.txt','wb') for protein in data: f.write(protein) f.write(',') f.write(json.dumps(data[protein])) f.write('\n') f.close() </code></pre> <p>If you are on windows and want to view the file as plain text, you may want to replace '\n' with '\r\n' or os.linesep. </p> <p>If you want to skip some rows (if there is a header or something), you can do something like this:</p> <pre><code>import csv import json data = {} rows_to_skip = 1 rows_read = 0 with open('proteins.csv','rb') as f: reader = csv.reader(f) for row in reader: if rows_read &gt;= rows_to_skip: name = row[0] sequence = row[1] mod_sequence = row[2] mod_indeces = map(int,row[3].split(', ')) spectral_count = int(row[4]) peptide = {'sequence':sequence,'mod_sequence':mod_sequence, 'mod_indeces':mod_indeces,'spectral_count':spectral_count} if name in data: data[name]['peptides'].append(peptide) else: data[name] = {'peptides':[peptide]} rows_read += 1 f.close() f = open('output.txt','wb') for protein in data: f.write(protein) f.write(',') f.write(json.dumps(data[protein])) f.write('\n') f.close() </code></pre> <p>If you want the keys of the dictionary to be in a particular order, you can use an orderedDict instead of the default dict. Just replace the peptide line with the following:</p> <pre><code>peptide = OrderedDict([('sequence',sequence), ('mod_sequence',mod_sequence), ('mod_indeces',mod_indeces), ('spectral_count',spectral_count)]) </code></pre> <p>Now the order is preserved. That is, <code>sequence</code> is followed by <code>mod_sequence</code> followed by <code>mod_indeces</code> followed by <code>spectral_count</code>. To change the order, just change the order of elements in the OrderedDict.</p> <p>Note that you will also have to add <code>from collections import OrderedDict</code> in order to be able to use OrderedDict.</p>
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    1. USMatthew Wesly
    1. USMatthew Wesly
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    1. COThank you Matthew! I saved your script in Python format and ran it from a terminal on Mac OS X. I received the following error, which could be on my part through running it, but I'll post it anyways:
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    2. COTraceback (most recent call last): File "/Users/zsyed/PythonPeptideJSON.py", line 8, in <module> for row in reader: _csv.Error: new-line character seen in unquoted field - do you need to open the file in universal-newline mode?
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    3. COAnd thank you for your feedback on my program. I will take into consideration what you said and try going through it again
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