fna file This is a topic that many people are looking for. newyorkcityvoices.org is a channel providing useful information about learning, life, digital marketing and online courses …. it will help you have an overview and solid multi-faceted knowledge . Today, newyorkcityvoices.org would like to introduce to you Reading FASTA files in python3 : Tut2. Following along are instructions in the video below:
“Again this is the second lecture in the python for biologists absolute beginner course and and in this lecture. I m going to introduce you to different ways or actually good way of reading faster files and searching for coding sequences in a faster file. So there are three main methods to deploy here the first one is using variable dot. Read the second one is to use read line.
The third one is to use read lines in python. So what i m going to go through in this lecture is to use variable dot read. Which is a method that allows you to read the contents of a faster file or any string containing file. So let s get started.
I saved the dna sequence file in this repository here. So this is the file in this folder and in order for you to get the path of this file. What you do is to click here and copy the path. This is quite simple you copy it so basically what you do is to click here and copy.
This highlighted region and then paste it in a variable. So let s say we have x variable and this is equal to open you can also use with open. But it is fine if you don t do it you paste the path then we write down the name of the file. So backslash the name of the file is do t not faster.
It s important to write down faster. Then you tell python to read. This is the purpose to read r. Means to read.
Whenever you open a file. It is critical for you to close it so you close the file now in between you write down code. So a is equal to x. Dot read.
And thus. What we need this is the first thing that you do you open the file. You really close it now run this code hold ctrl and press enter or hold shift and press enter now if it doesn t return error. It means that everything went smoothly.
Now once we read the file you can print it out well this gives you an output let s see the output. The first line until here is the first information line. Which we don t need here we have to remove it so if you have a look at the file and try to count the first line is 103 characters and we don t want that we have to remove it this is the first test that we do then you have return characters in every line. So this is called carriage return characters and we ve got to delete these as well we don t do it manually this is a programming language.
We do it the easy way so the first thing to do is to remove the first 103 characters we create a variable and declare a variable. You say b is equal to a and this is from 103 to the very end then you can now. See what b looks like so v. Looks like this which has the first line removed from the fasta file.
Now we declare another variable called c. Well. I m trying to do it incrementally. So that you understand each step.
The easy way c. Is equal to b. Dot r. Applies.
So we replace the returned characters with empty strings. So this is the first argument and you just write something like this two quotations. Without any space in it and now. Let s see what c.
Contains so c. There is no return character left. Now we can use this variable and try to get some information out of it if you have a look at the fasta file from the ncbi database. You can see that there are information about the coding sequences.
Now we are going to retrieve the first coding sequence and the information for the first coding sequence is highlighted here this is the first coding sequence now we would basically search for the beginning at the end of the dna sequence containing the coding sequence. So basically this is the beginning beginning equals to this one and we want to capitalize this so beginning capitalized is equal to the beginning sequence dot upper. So the upper method here what what it does is it makes every character here uppercase letters. We do the same for the ending.
So we take this part. We say ending equals this one and and capitalized equals. The same thing so dot upper now once we run this we actually get all of these capitalized now those two are capitalized so let s see where these two are in our plain dna sequence here a good method here to use is find method so what you do is to write down c. Dot.
Find basically we can write down e and b. We. See means. Beginning of c.
Equals. C. Dot. Find the beginning.
So this finds. The index value over the beginning. You can also write beginning index. So that s easier for you to understand what s going on ending index equals c.
Don t find the ends capitalized. So we search for these two within the variable c. So. What we do here is that we have a variable called c.
And it contains your dna. So we search c for the beginning and the end to mark the beginning and the end of the dna sequence. So what we have here is the beginning. We put the beginning here the index and the end there in between is filled with the coding sequence.
Which is the first coding sequence now we want to print out see print see from the beginning index to the ending index so this is how you reference it basically you can also say something here to tell the user that this is this is the first coding sequence. You can also have a return character to avoid mixing it and it tells you this is the first coding sequence from atg to gtc so let s see why gtc. This is because gtc was the beginning so it returns. The beginning now we have one two three four five characters left so in this case.
What we do is to actually incremented by characters so you write down endings equal ending index plus eight da. There you go so eight characters after this one gtc. It was actually this one gtc you have eight characters then you are returned with the proper coding sequence. So this is the coding sequence.
This is how you are returned with the coding sequence you can do it other ways. There are lots of different other ways to do so. But this is a basic way a kind of a hard coded easy way of finding otherwise you can basically try to retrieve xml file. So here you have xml file and from the xml file you have you can easily take out every piece of information like the coding sequence you just write down the coding sequence.
And it returns this for you in one instance. But this is important for you to understand how the fasta file works and how to retrieve dna sequences and parts of dna sequences from fasta file. I hope you enjoyed the lecture and thank you ” ..
Thank you for watching all the articles on the topic Reading FASTA files in python3 : Tut2. All shares of newyorkcityvoices.org are very good. We hope you are satisfied with the article. For any questions, please leave a comment below. Hopefully you guys support our website even more.