No in the case of python ,  I have been writing scripts that take in user input from the command line for a while now. In these scripts , I would generally accept only one input and that would be the first in the sys.argv list. If I had more than one input I would iterate over the input list and try and figure out what the inputs were . Even worse in most cases I would  hard code the order  of inputs into my code ( terrible practise). Fortunately  for me , my discovery of the optparse module has changed all that.

The optparse module is  an object oriented ( dont let that scare you) and super-intuitive way to add command line options to any python scriptSo say you want to add an input file command line switch with the -i attribute , All you have to do is

from optparse import OptionParser

optparse_object =OptionParser()

optparser_object.add_option(“-i”,”–infile”, dest=”infile”,help=”input file for script” , metavar=”[infile.txt]“)

Once you do this you can easily have the module parse the sys.argv list and make sense of it .So you would add the following line

options_object, spillover_options = optparser_object.parse_args()

Then options_object.infile  will have the value of the input option . This is specified by the dest section in the add_option argument list) . The nice thing with the module is that all possibilities can be mapped to the same options_object.infile destination . So for eg I have mapped “-i” and “–infile” to the same destination .Even better is the option to add a help string with the help=”help text” argument . This help is then printed out if the user provides an option that the script cannot handle or if the code specifically calls  the optparser_object.print_help() function.

For a concrete example on how to use the opt_parse module consult the docs or my example code on github .

Well today I was forced with a rather simple task. I had to order a primer for a sub-cloning experiment that was the reverse primer corresponding to the last twenty bases of a given protein coding gene sequence.

Here is how python made the task super easy

1) First I opened the pubmed page with my sequence and copied the forward strand to my interactive python session

2) Then I wrote a couple of  lines to generate the reverse complement at the same time reversing the order of the string

So in the above example the

Is the reverse complement dictionary. The for loop replaces each nucleotide with its complement and simultaneously reverses the order , because every nucleotide is added to the begining ( i.e prepended) . So the last nucleotide ends up first.

The other way to do the same thing would be to use python string reversal as demonstrated in the code below

The cool part here is the funky and admittedly unreadable string-reversal syntax,

So In python string reversal is powerful. The p[::-1] basically says , give me the string from start to finish in backwards order (-1) . This elegant string reversal in python is explained well in this post and gives us the primer sequence in the correct 5-prime to 3-prime order as required by the oligo-synthesizing order forms.