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POIterating through a list where I have to grab data from the first item for use in the last item
 

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  1. POIterating through a list where I have to grab data from the first item for use in the last item
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    <p>This is a follow-up to a previous question I had asked: <a href="https://stackoverflow.com/questions/14063387/processing-a-sub-list-of-variable-size-within-a-larger-list">Processing a sub-list of variable size within a larger list</a>.</p> <p>I managed to use itertools to get groups of DNA fragments out, but now I'm faced with a different problem. </p> <p>I need to design primers based on these groups of DNA fragments. Primers are designed by including overlaps from different DNA fragments. Let's say I have three DNA fragments in a list, fragments A, B, and C. I need to extract:</p> <ul> <li>the last 20 nucleotides (n.t.) of C to concatenate (in order) with the first 40 n.t. of A,</li> <li>the reverse complement (RC) of the first 20 n.t. of B to concatenate in order with the RC of the last n.t. of A,</li> <li>the last 20 n.t. of A to concatenate with the first 40 n.t. of B,</li> <li>the RC of the first 20 n.t. of C to concatenate with the RC of the last 40 n.t. of B,</li> <li>the last 20 n.t. of C to concatenate with the first 40 n.t. of A,</li> <li>the RC of the first 20 n.t. of A to concatenate with the RC of the last 40 n.t. of C.</li> </ul> <p>I can't seem to solve this problem, and I'm not sure where's the best place for me to start on this... </p> <p>Code that I've already written so far outputs just "group 1" (on purpose, so I can minimize the amount of visual output I'm dealing with). Here it is:</p> <pre><code>#import BioPython Tools from Bio.Seq import Seq from Bio.Alphabet import IUPAC #import csv tools import csv import sys import os import itertools with open('constructs-to-make.csv', 'rU') as constructs: construct_list = csv.DictReader(constructs) def get_construct_number(row): return row["Construct"] def get_strategy(row): return row["Strategy"] ## construct_list.next() ## construct_number = 1 primer_list = [] ## temp_list = [] ## counter = 2 groups = [] ## for row in construct_list: ## print(row) ## for key, items in itertools.groupby(construct_list, key=get_construct_number): for subitems in items: #here, I am trying to get the annealing portion of the Gibson sequence out if subitems['Strategy'] == 'Gibson' and subitems['Construct'] == '1': print(subitems['Construct']) fw_anneal = Seq(subitems['Sequence'][0:40], IUPAC.unambiguous_dna) print(fw_anneal) re_anneal = Seq(subitems['Sequence'][-40:], IUPAC.unambiguous_dna).reverse_complement() print(re_anneal) fw_overhang = Seq(subitems['Sequence'][0:20], IUPAC.unambiguous_dna).reverse_complement() print(fw_overhang) re_overhang = Seq(subitems['Sequence'][-20:], IUPAC.unambiguous_dna) print(re_overhang) </code></pre> <p>Any help would be greatly appreciated!</p>
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    1. USericmjl
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    1. COOne approach would be to first design a little domain-specific language that could be used to express the combinations in each of the 6 extractions in a formulaic way. Next implement an interpreter to parse, evaluate, and compute the result of such an expression given three DNA fragments designated as A, B, & C. Once that is working you should then be able to apply such expression any combination of fragments -- such as those you generating. There are many tools avaiable to help you evaluate [little languages](http://c2.com/cgi/wiki?LittleLanguage), an idea that's been around a long time.
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    2. COIs there no way to be able to do this in Python? (My apologies, I'm not very fluent in programming, kinda just above beginner level here...)
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    3. COI was assuming you would implement it in Python.
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