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Blake Allen
Добавлен 28 мар 2013
Python 3 & Python 2.7 dual install - the right way on OSX
Python 3 & Python 2.7 dual install - installing Python 3 the right way, if you want to get started programming in Python, It's very important that you install Python the right way. This tutorial will show you how to use Home brew to install Python.
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Видео
Your First Program And Variables in Python
Просмотров 97311 лет назад
Getting Started in Python - after you've installed Python3 you're ready to start making your own programs. In this Tutorial we'll learn what a variable is and how to print them using Python3.
Python for Bioinformatics - Python As A Calculator
Просмотров 4,9 тыс.11 лет назад
Using Python as a Calculator - Learn the basics of using Math in Python
What is Bioinformatics
Просмотров 10 тыс.11 лет назад
For more information visit: www.howtobioinformatics.com
Python For Bioinformatics and Your First Python for Bioinformatics Program
Просмотров 105 тыс.11 лет назад
For more in-depth Python for Bioinformatics training visit: www.howtobioinformatics.com/pythonforBioinformatics Hi and welcome to Python for bioinformatics, my name is Blake Allen, and I am going to show you how to make your first Python for Bioinformatics program, in under 20 minutes. Were going to go over calculating GC content and making your first Python Program, So if you're a little more ...
The best video i have seen on bioinformatics
thanks it is very good information
Thank You!
Why never start with the code this man?
oh man, wow thanx
Just small question. Is this what bioinformatics mostly do? Sequence genes then use a programming language for analysis?
In a nutshell...YES. But in addition to analysis, they can use programming for drug discovery therapeutics. They can use programming for predictive analytics to see if something will switch a gene on or turn it off before administering it experimenting with it to save time and money.
good work
My syntax is always error in If char == "g" : Usually in (if) and in (g) Help me why
'g', you need to check for a char not a string
invalid syntax on the second quote of print "number of g's " + str(g)
idk if its because he's using make but If you are using windows like I am, make sure that when you use the "print" function, make sure to use parenthesis Ex: (EXACTLY LIKE THIS) print("number of g's " + str(g)")
Same here, thank you so much for the advice I am going to try it
I think the syntax changed in Python3
Спасибо тебе большое за этот разбор!
this is outstanding iam hoping you can show more examples in jupyter notebook
very nice
Thank you it works very well
Hello, Thanks for this video! I was wondering if we could use the difflib program to do comparative genomics for two different files and create a report of differences?
9:00 variable*
Pls provide the exact link for dataset download in description
any more advanced python scripts to use for the analysis of sequencing data
👏👏👏
I very much enjoyed this video. I like the fact that, by the end, I'm working with real data and doing something useful. Thanks!
What version of python did you use?
1.75x Speed would be really appreciated for this video :D
amazing simple and straight forward tutorial. here's the dna link www.ncbi.nlm.nih.gov/nuccore/359465566?report=fasta here's the code to try it out : #comment #calculate CG content gene = open ("BRCA1_BAP1.txt", "r") #setting values to 0 g=0; a=0; c=0; t=0; #skip first line of header gene.readline() for line in gene: line = line.lower() for char in line: if char == "g": g+=1 if char == "a": a+=1 if char == "c": c+=1 if char == "t": t+=1 print ("number of g's " + str(g)) print ("number of c's " + str(c)) print ("number of a's " + str(a)) print ("number of t's " + str(t)) # 0. = convert to floating point gc = (g+c+0.) / (a+t+c+g+0.) print ("gc content: " + str(gc))
Someone should re-do these videos in Windows.
for beginners only
Why the fuck you click so hard on that mouse. I do not like ur style at all. You seem like a spoiled brat.
What is bioinformatics plz tell its basic .
super inneficient code. use the count() funcion which is WAY faster!
I timed both ways on a file of 117k bases. His way used 0.02 sec. Using count() used 0.005 sec. Both are fast enough for me.
@@georgegrevera7000 The problem is scale. Had the gene sequences been longer, this would be exponentially inefficient. I'm coming from a computer science background though, where efficiency is hammered into our heads due to scalability
gc = 0 for base in gene: if base = 'G' or base ='C': gc += 1 return float(gc)/len(gene) In PCR experiments, the GC-content of primers are used to predict their annealing temperature to the template DNA. A higher GC-content level indicates a higher melting temperature. wiki / gc content
Thanks a lot, it was really helpful. You haven't put any other videos on this subject since 2013, though.
dude why does this not work at all using windows
did you install python?
yes
Matt saying it doesn't work "at all" isn't really a helpfull comment.
It is really helpful. Thanks!
thanks so much i'll definitely be coming back
poor video making quality
bevkuff
Why not write it in the Python IDLE?
Why not use count() or regular expressions?
poor Python skills
No, poor programming skills.
Nice cool intro to bioinfo
which python book could be better for references ? This is nice!
Thanks but I had problem while running. I used windows bash and I got " print "number of g's " + str(g) ^ SyntaxError: invalid syntax error. Even though I did the same thing that you did. Please help me
+Suleyman Bozkurt That maybe because you are using python 3+ where the syntax for print statement is print("number of g's "+ str(g)) [Notice the parentheses], whereas in python 2+ the syntax for print is as mentioned in the video[ print "number of g's " + str(g) ] Hope it helped! :)
thnx boss. resolved my issues.
why not use macports instead?
+Surya Avinash Avala because it sucks :o)
This is nice. A more advanced and brief way to count bases would be by using a Counter. Here is an example: gist.github.com/sunworshipper/0de4cc762467b849c727
anyone know the answer ? what ,if u take the fasta format without head ,can u get rid of that gene.readline() ? And when the counter are named with A,C,T,G string, can u get rid of that line.lower() ? TQ 4 any suggestions .
+willie ekaputra yeah that just skips the line, so if the line is not there you don't need to skip it, but if you remove it then it's no longer a fasta file. Either way, this is not how an advanced Bioinformatician would solve this task.I think Blake is showing that you can make the string lower case. It usually is upper case so you don't need to be converting you don't need that line.
I have other question, can u then make this code a fct . with Def ... () :, so that u can open ANY Fasta saved files in yer PC and count its GC Content ?
Awesome, my first python program to know the gc content... I have a question, What is the gc content for? What does it tell me exactly? Did not understand that very well. BTW I used this squence Rattus norvegicus BRCA1 mRNA, complete cds gc content: 0.460014
Thanks a lot for a nice turotial! But have you tried TextWrangler instead of Textedit?
Really helpful! I love Python!
How is it one can discover the relative platform of" program" terminals. As I kid I had access to cmd. Or something like that, I didn't know what I was doing, but to search for a terminal, how might that be done?
Hi, So I wrote the same program on PyCharm I tried opening this in Bash Shell and I get told "not a directory". I switched directories to ensure I was in the right folder. Does anyone have suggestions?
Very helpful, thanks!
very straight forward tutorial, thanks
Thanks for the help! :)