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Titlerescued by code!

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Description rescued by code provides a variety of resources — paid and free — that are designed to teach people to use unix and to write code. in particular, our material is particularly aimed at those working in...

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Keywords unixandpython,python,perl,writing,programming
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perl vs python: printing variables
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python 2 vs 3: all hail the print function
perl vs python: the print function and newlines
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my python origin story
the perils of learning a new programming language
lessons learned while writing a book about programming
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archive /archive
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1 #fn:p146099418328-exact_versions
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1 #fn:p145357285978-python_breadth
2 #fn:p145357285978-zen_breaking
#fnref:p145357285978-python_breadth
#fnref:p145357285978-zen_breaking
older → /page/2
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about the authors /about-the-authors
unix & perl to the rescue — the book! /unix-and-perl-book
unix & perl primer for biologists — free! /unix-and-perl-primer
linux bootcamp — free! /linux-bootcamp
rss /rss
random /random
archive /archive
mobile /mobile

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rss http://rescuedbycode.com/rss
ongoing series of posts http://rescuedbycode.com/post/145222493368/lessons-learned-while-writing-a-book-about
keith bradnam http://t.umblr.com/redirect?z=%255bhttp%3a%2f%2fwww.keithbradnam.com%255d%28http%3a%2f%2fwww.keithbradnam.com%2f%29&t=zja4yzexmwzimmexzdexmdjkzjzkmdyzymfjytg1m2y1mtu5m2nmncxndk1kr3y4eg%3d%3d&b=t%3aoekwarhey73mhe6nklzj_g&m=1
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perl to python http://rescuedbycode.com/tagged/perlvspython
python 2 and 3 http://rescuedbycode.com/tagged/python2vs3
my previous post http://rescuedbycode.com/post/145608314273/perl-vs-python-the-print-function-and-newlines
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3 months ago http://rescuedbycode.com/post/150136648533/perl-vs-python-printing-variables
1 http://rescuedbycode.com/post/150136648533/perl-vs-python-printing-variables#notes
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ongoing series of posts http://rescuedbycode.com/post/145222493368/lessons-learned-while-writing-a-book-about
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perl to python http://rescuedbycode.com/tagged/perlvspython
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many technical reasons http://t.umblr.com/redirect?z=https%3a%2f%2fwww.python.org%2fdev%2fpeps%2fpep-3105%2f&t=yza5mzfmm2njmjjizwq1ywm5zgfjogewzgfkmziwmmm5mwuwmdjkyswxbm9mmem5bq%3d%3d&b=t%3aoekwarhey73mhe6nklzj_g&m=1
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5 months ago http://rescuedbycode.com/post/146099418328/python-2-vs-3-all-hail-the-print-function
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ongoing series of posts http://rescuedbycode.com/post/145222493368/lessons-learned-while-writing-a-book-about
keith bradnam http://t.umblr.com/redirect?z=%255bhttp%3a%2f%2fwww.keithbradnam.com%255d%28http%3a%2f%2fwww.keithbradnam.com%2f%29&t=mzfhntuzoge0oddhzjbmnje5nduxmtjhzgy4odbizgrmzgi3ytawmcxiclg2vmowsg%3d%3d&b=t%3aoekwarhey73mhe6nklzj_g&m=1
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6 months ago http://rescuedbycode.com/post/145608314273/perl-vs-python-the-print-function-and-newlines
2 http://rescuedbycode.com/post/145608314273/perl-vs-python-the-print-function-and-newlines#notes
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ongoing series of posts http://rescuedbycode.com/post/145222493368/lessons-learned-while-writing-a-book-about
keith bradnam http://t.umblr.com/redirect?z=%255bhttp%3a%2f%2fwww.keithbradnam.com%255d%28http%3a%2f%2fwww.keithbradnam.com%2f%29&t=ztvmndm3m2i2yjq4ytizyzqxymy2njrhyjniyzdjntqzowm4yjlkncxtohvdqxfauw%3d%3d&b=t%3aoekwarhey73mhe6nklzj_g&m=1
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perl to python http://rescuedbycode.com/tagged/perlvspython
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“unix and python to the rescue!” http://rescuedbycode.com/post/124667553478/we-are-writing-a-new-book-unix-and-python-to-the
python for data analysis http://t.umblr.com/redirect?z=http%3a%2f%2fshop.oreilly.com%2fproduct%2f0636920023784.do&t=zdhmnju4zgixmmi5yjyyzwflmzk1ntm0zdawmtdlodi5ndziotjlyyxtohvdqxfauw%3d%3d&b=t%3aoekwarhey73mhe6nklzj_g&m=1
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6 months ago http://rescuedbycode.com/post/145357285978/my-python-origin-story
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ongoing series of posts http://rescuedbycode.com/post/145222493368/lessons-learned-while-writing-a-book-about
keith bradnam http://t.umblr.com/redirect?z=%255bhttp%3a%2f%2fwww.keithbradnam.com%255d%28http%3a%2f%2fwww.keithbradnam.com%2f%29&t=nzhlnzziowe5mtbimmm1n2rlztc1zwfhmgrkn2qyngmwzmfjnjyynixzszj1efdpsw%3d%3d&b=t%3aoekwarhey73mhe6nklzj_g&m=1
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6 months ago http://rescuedbycode.com/post/145323782793/the-perils-of-learning-a-new-programming-language
2 http://rescuedbycode.com/post/145323782793/the-perils-of-learning-a-new-programming-language#notes
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we are currently writing a book about learning python http://rescuedbycode.com/post/124667553478/we-are-writing-a-new-book-unix-and-python-to-the
unix and perl to the rescue! http://t.umblr.com/redirect?z=https%3a%2f%2fwww.amazon.co.uk%2funix-perl-rescue-keith-bradnam%2fdp%2f0521169828%3ftag%3dkeithbradnamc-20&t=ogm5nwzlzgm1ntbkzjvlzdjhnzbjotflodnmyzhjmmrjnwriotdmysxvbxrocwz6aq%3d%3d&b=t%3aoekwarhey73mhe6nklzj_g&m=1
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the perils of learning a new programming language http://rescuedbycode.com/post/145323782793/the-perils-of-learning-a-new-programming-language
my python origin story http://rescuedbycode.com/post/145357285978/my-python-origin-story
perl vs python: the print function and newlines http://rescuedbycode.com/post/145608314273/perl-vs-python-part-1-the-print-function-and
python 2 vs 3: all hail the print function http://rescuedbycode.com/post/146099418328/python-2-vs-3-all-hail-the-print-function
perl vs python: printing variables http://rescuedbycode.com/post/150136648533/perl-vs-python-printing-variables-this-is-part
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archive rss perl vs python: printing variables this is part of an ongoing series of posts by keith bradnam and michelle gill that chronicle some lessons that we have learned while writing unix and python to the rescue! keith will be discussing his experiences in switching from perl to python while michelle will cover differences between python 2 and 3.after mastering how to print ‘hello world’, one of the other immediate things you want to do with any programming language is to learn about using variables…and how to print them. let’s look at a really simple example and contrast how we might do this in both perl and python: # perl my $answer = 42; print "the answer is $answer\n"; # python answer = 42 print('the answer is', answer) i don’t think there is too much complexity with either language here. you can, of course, write a perl solution in a similar way to python: # perl v2 my $answer = 42; print "the answer is ", $answer, "\n"; the print functions of both languages allow you print a comma-separated list of items. note how python joins items together with a space character by default ( so no space is needed after 'is’) whereas perl doesn’t. of course, with perl you have to include a newline unless you use the say function (see my previous post for more details).so far, so good. but what happens when you want to increase the complexity of the print statement just a little bit? # perl my $max_volume = 11; my $increment = 1; print "$max_volume is $increment louder than 10\n"; # python max_volume = 11 increment = 1 print(max_volume, 'is', increment, 'louder than 10') even with two variables, the python print statement starts looking a little more ugly. this is where perl’s easy 'variable interpolation’ — substituting variables for their underlying values — helps make for cleaner looking print statements.of course, there are other ways of printing multiple variables in python: # python v2 max_volume = 11 increment = 1 print('%d is %d louder' % (max_volume, increment)) this is python’s string expression printing method and is something that appears widely in examples of 'how to print variables in python’ online. however, python has another method of printing variables using something called a string formatting method: # python v3 max_volume = 11 increment = 1 print('{:d} is {:d} louder'.format(max_volume, increment)) this string formatting method is, as its name suggests, a method that is applied to a string in order to format it. the placeholders above {:d} indicate that the variable should be a digit, but we could also simplify this to just use {} instead.it is possible that this newer technique for printing variables will fully replace the older string expression method which may become deprecated. in any case, you should be aware that there are two distinct styles that you may see in use for printing variables in python.summarythis has been one area where my perl experience led me to struggle with learning how to print variables in python. it takes longer to learn and is confusing when you have two different ways of achieving the same goal.perl’s style of variable interpolation would not be possible in python because python variables do not start with any special character that helps distinguish variable names from regular words. #unixandpython #perl #python #print #variables #perlvspython 3 months ago 1 permalink share short url twitterfacebookpinterestgoogle+ python 2 vs 3: all hail the print function this is part of an ongoing series of posts by keith bradnam and michelle gill that chronicle some lessons that we have learned while writing unix and python to the rescue! keith will be discussing his experiences in switching from perl to python while michelle will cover differences between python 2 and 3.one of the more well-known changes in python 3 is the upgrading of print from its lowly python 2 status as a statement to a genuine, first-class function in python 3. in most cases, this simply means a set of parentheses need to be added.here is an example using the print statement from python 2: # python 2 uses a print statement print 'the castle of aaarrrrggh.' and here is the same example adapted for python 3: # python 3 uses a print function print('the castle of aaarrrrggh.') as we will learn in “unix and python to the rescue!”, later versions1 of python 2 have a future module that allows you import things from the future (python 3). what’s more, python 3 code will run just fine with this import, albeit without any actual changes since python 3 is the future. this means you can write code that is version independent using the future module.here is an example of the above code written in a way that is independent of python 2 vs 3: from __future__ import print_function # python 2 and 3: print('the castle of aaarrrrggh.') now that we understand how to update code to work with python 3, we might want to know why this is useful. there are actually many technical reasons, but the main one is consistency with other functions. in python 2, print was something of an outlier in that it often worked like a function, but not always. and its syntax reflected this.for example, the following code produces an error in python 2: [print x for x in range(5)] # python 2: # syntaxerror: invalid syntax however, this will work in python 2 (and 3) when print is an actual function: from __future__ import print_function [print(x) for x in range(5)] # python 2 and 3: # 0 # 1 # 2 # 3 # 4 this introduction is intended provide a basic understanding of one of the most commonly encountered differences in python 2 vs 3 and explains why the change is—in most cases—an improvement. it’s also important to understand how to write code that is independent of which python version is being used.the future module is implemented starting with python 2.6. ↩ #unixandpython #python #print function #coding #python2vs3 5 months ago 1 permalink share short url twitterfacebookpinterestgoogle+ perl vs python: the print function and newlines this is part of an ongoing series of posts by keith bradnam and michelle gill that chronicle some lessons that we have learned while writing unix and python to the rescue! keith will be discussing his experiences in switching from perl to python while michelle will cover differences between python 2 and 3.when learning any programming language, the first coding example we always learn is how to write a program that will simply print the words'hello world’. in perl, we would use the print function as follows: print "hello world!\n"; whereas in python (version 3), we would use: print('hello world!') the principle difference being that in perl you have to explicitly include a newline character (\n) as part of the printed string whereas python gives this to you for free. the other obvious differences are python’s requirement of parentheses (in version 3) and perl’s requirement of a semicolon.you don’t have to include \n in perl, but without it your printed output will probably not be what you want. in version 5.10 (from 2007), perl introduced a say() function as an alternative to print(), and this function lets you omit the newline: say "hello world!"; # includes newline for free! the say() function wasn’t introduced until long after i had started using perl, and including \n in print functions is a hard habit to break when you’ve been using it for a decade or so.an issue with perl’s approach is that newlines can be a bit of a confusing topic to explain to people who are new to programming. however, perl’s print() function is at least explicit…no newline character in the code, no newline in your printed output.this raises the question…how do you not include a newline when printing in python? the solution in python (version 3) is to use the ‘end’ argument to the print() function which lets you specify what the 'end’ character will be…in this case, we want to remove the default end character (\n): print('hello world!', end = '') summaryi find perl’s method for printing more explicit, even with the added cost of having to explain to a new programmer what the deal with \n is. python’s approach is more readable…until you want to omit the newline. #unixandpython #perl #python #print #newline #perlvspython 6 months ago 2 permalink share short url twitterfacebookpinterestgoogle+ my python origin story this is part of an ongoing series of posts by keith bradnam and michelle gill that chronicle some lessons that we have learned while writing unix and python to the rescue! keith will be discussing his experiences in switching from perl to python while michelle will cover differences between python 2 and 3.all superheroes need an origin story. while i don’t consider myself a superhero, the title and theme of our forthcoming book, “unix and python to the rescue!” depicts one. and i think there is some truth to this depiction—learning to program is a challenging undertaking, but once you have acquired a few basic skills, you can do incredible things with your data. in that spirit, i would like to share what i call “my python origin story.”my introduction to programming came rather serendipitously during my senior year of high school. i’d finished all the math courses offered by my rural high school the previous school year. not knowing what else to do with me, my math teacher offered to teach me how to program during his lesson planning period. the arrangement worked quite well—he’d teach me a short lesson for the first fifteen minutes of the period and then send me off to practice. i learned pascal this way and then advanced basic.in college, i added to my growing repertoire of languages by learning fortran 95 as part of the requirements for my chemical engineering major. despite multiple opportunities, programming didn’t really “stick.” maybe i hadn’t yet found a language i liked, or maybe i simply didn’t have a compelling use for it.both of these things changed when i was a graduate student. as a structural biologist, i was constantly performing text manipulations, such as conversions between file formats and switching naming conventions for atoms in pdb files. i discovered some perl scripts from a former labmate that facilitated a few of these tasks, so i learned perl in order to tailor them for my own use. programming proved to be quite handy and quickly developed into one of my favorite research tasks.during my time as a postdoctoral researcher, i learned a new language—python—so i could write some custom functions for a program that was popular in the lab. this coincided with a very exciting time in the python scientific community. numpy had been released a few years earlier and other python scientific packages were also maturing. i learned how to perform non-linear regression using scipy and visualize the results using matplotlib. python provided what i considered to be the best of both perl and fortran—powerful text processing and robust linear algebra functions 1.towards the end of my time as a postdoctoral researcher, i read wes mckinney’s python for data analysis and learned pandas. the object-oriented nature of pandas’ methods clicked with me, and i still use the library whenever possible. despite having learned pandas some years ago, i constantly discover new ways of accomplishing common tasks 2.sharing this love of python with others is one of my reasons for joining keith and ian in writing “unix and python to the rescue.” as work on the book has progressed, i have learned new things myself, not the least of which is finally completing my switch from python 2 to python 3. i look forward to sharing these lessons with you in the coming weeks.i think this observation helps to explain some of the popularity of python. it may not always be the best tool for the job, but it is usually a very good one. ↩acknowledging more than one way to do things may go against the zen of python, but i say rules were meant to be broken. ↩ #unixandpython #python #basic #fortran #matplotlib #pandas #programming #perl 6 months ago 1 permalink share short url twitterfacebookpinterestgoogle+ the perils of learning a new programming language this is part of an ongoing series of posts by keith bradnam and michelle gill that chronicle some lessons that we have learned while writing unix and python to the rescue! keith will be discussing his experiences in switching from perl to python while michelle will cover differences between python 2 and 3.as a kid, my first real experience with programming was of the variety: 10 print "hello" 20 goto 10 at the time, my computer was a bbc micro — yes i’m getting old — and i never really spent the time to learn much more basic than in the example above. i do remember learning enough to be able to disable the escape and break keys on the bbc micro. this meant that we could go to our local shop that sold computers (currys) and write annoying programs on their public computers that couldn’t easily be halted.it wasn’t until much later when i was studying for my masters degree in bioinformatics that i really started to learn a programming language. any bioinformatician starting out today would probably gravitate immediately to python, perhaps with some r thrown in for good measure. however, back in 1993 — a time when the world wide web barely existed — the language we learnt was c++.i have strong memories of really hating c++. or maybe i just didn’t enjoy the style of the instructor. there seemed to be so much to learn before you could do anything useful. i learnt enough to be able to help write a few programs, one of which was used to process the output from a multiple sequence alignment program. this involved a lot of text parsing which didn’t seem to be a particular strength of c++ at the time.fast forward a couple of years and in october 1996 i started my phd which was to look at the new world of eukaryotic genome sequence analysis (at the time there was only one complete eukaryotic genome!). on my first day i remember a lab colleague handing me a copy of learning perl and imploring me to ‘learn this quickly’.this was in the days of perl version 4. i think hashes were still being called 'associative arrays’ and there was very little you could do in perl in an object-oriented fashion.i loved perl. it was everything that c++ wasn’t. great for working with text, not fussy whether a variable contained a single digit, a string of words, or a very long floating-point number. i also enjoyed a lot of the subtle touches of humour in the learning perl book. i seem to recall the die function being introduced with the following example: die "you gravy sucking pigs" so perl was my first real (programming) love and i stuck with perl for most of the next couple of decades. the danger of learning a programming language at a time when it was still evolving is that you learn some bad habits, and learn to do things in ways which will later turn out to be suboptimal.this all brings us to today. having co-authored a book on perl, i am now trying to co-author a follow up which will instead focus on python. this seems to the language of choice now for anyone starting out in bioinformatics. these days it feels wrong to think of bioinformatics as a separate discipline, it’s just a set of skills which are increasingly being learnt by undergraduates of many different biological disciplines.i am not a python programmer. you may think this is a bit of a problem for someone trying to write a book about the python programming language and you would be correct! so we are enlisting the assistance of someone who does know how to program in python: step forward michelle gill! she will hopefully keep ian korf — my co-author from unix and perl to the rescue! — and myself on the correct path of python purity.i am in the process of learning python to assist with the writing of this book and it struck me that it may be useful to share some of my experiences as i learn new tricks and unlearn old (perl-based) habits. i’ve already had many 'aha!’ and 'what-the-what?!?’ moments and i plan to write a series of short lesson as, and when, i come across issues. #unixandpython #python #perl #book #writing #programming #unix 6 months ago 2 permalink share short url twitterfacebookpinterestgoogle+ lessons learned while writing a book about programming as you probably know if you’ve been following this blog, we are currently writing a book about learning python. this is intended as a follow-up to the 2012 book unix and perl to the rescue!. this new book is primarily being written by keith bradnam and michelle gill, with assistance from ian korf.as we draft the chapters and excercises for this new book, we have reflected on — and sometimes even learned! — certain aspects about the python programming language and how it compares to perl.we thought it might be fun and instructive to share some of these thoughts here. over the next few months, we will take turns sharing some of these observations in short blog posts. keith will focus on differences between python and perl, while michelle will note important differences between versions 2 and 3 of python — though our book is written with python 3 in mind, there are still many situations where python 2 is being actively used in computing.we aim to bring you a new post every week or two and we will start off by providing a little bit of background about how we developed our programming skills.poststhe perils of learning a new programming language — keith explains his introduction to the world of programmingmy python origin story — michelle reveals her own path to becoming a programmerperl vs python: the print function and newlinespython 2 vs 3: all hail the print functionperl vs python: printing variables #unixandpython #python #perl #unix #writing 6 months ago permalink share short url twitterfacebookpinterestgoogle+ page 1 of 3 ← newer • older → about rescued by code provides a variety of resources — paid and free — that are designed to teach people to use unix and to write code. in particular, our material is particularly aimed at those working in the biological sciences and assumes no prior knowledge. we believe that everyone can learn how to code, and that coding can be fun! pages about the authors unix & perl to the rescue — the book! unix & perl primer for biologists — free! linux bootcamp — free! twitter @rescuedbycode on twitter rss random archive mobile this work is licensed under a creative commons attribution 4.0 international license (cc by). effector theme — tumblr themes by pixel union


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Here you can find chart of all your popular one, two and three word phrases. Google and others search engines means your page is about words you use frequently.

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