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POawk in python: How to use awk scripts in a python class?
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  1. POawk in python: How to use awk scripts in a python class?
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    copied!<p>I am trying to run an awk script using python, so I can process some data.</p> <p>Is there any way to get an awk script to run in a python class without using the system class to invoke it as shell process? The framework where I run these python scripts does not allow the use of a subprocess call, so I am stuck either figuring out a way to convert my awk script in python, or if is possible, running the awk script in python.</p> <p>Any suggestions? My awk script basically read a text file and isolate blocks of proteins that contains a specific chemical compound (the output is generated by our framework; I've add an example of how does it looks like below) and isolate them printing them out on a different file.</p> <pre><code> buildProtein compoundA compoundB begin fusion Calculate : (lots of text here on multiple lines) (more lines) Final result - H20: value CO2: value Compound: value Other Compounds X: Value Y: value Z:value [...another similar block] </code></pre> <p>So for example if I build a protein and I need to see if in the compounds I have CH3COOH in the final result line, if it does I have to take the whole block, starting from the command "buildProtein", until the beginning of the next block; and save it on a file; and then move to the next and see if it has again the compound that I am looking for...if it does not have it I skip to the next, until the end of the file (the file has multiple occurrence of the compound that I search for, sometimes they are contiguous while other times they are alternate with blocks that has not the compound.</p> <p>Any help is more than welcome; banging my head for weeks now and after finding out this site I decided to ask for some help.</p> <p>Thanks in advance for your kindness!</p>
 

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