[Python] Add pushback capacity to generators
Generators are a special kind of functions which return values using the keyword yield. The function itself is actually an iterator, allowing traversing its returned values in a for loop.
Sometimes, one may want to push back a obtained value to the generator and read again next time. To do so, one can create a iterable class to wrap generators. Below is an example:
A generator First, let’s construct a generator.
[R] minfi ERROR; return code from pthread_create() is 22
minfi is an R package to analyze DNA methylation arrays, such Illumina 450K and EPIC arrays.
One main function in the minfi package is estimateCellCounts; it can be used to estimate immuno cell fractions from a sample based on DNA methylation values. However, recently when I tried to run the function, I met the following problem during the normalization step:
1 2 3 4 5 6 7 8 9 10 Loading required package: FlowSorted.
[Linux] Caution: using command 'less' on gzipped file
A couple of years ago, I found that I can use Linux command less to view gzipped file, such as:
1 less in.gz This is very convenient to view gzipped file content.
However, recently, I noticed a problem with it. For a file which has 42196516 lines, if I opened it with less, it gave me a count of 30356021 lines:
1 2 less test.fq.gz | wc -l; # giving 30356021 gzip -dc test.
[Tips] Get the OS version of Linux
There are many variants of Unix/Linux systems, such as Ubuntu, Redhat, and even some versions in Windows system such as MinGW/Msys and Cygwin.
Today I am going to introduce a way to get such information, which is simple, run the following command
1 uname -o Running this command in Ubuntu and Redhat will yield GNU/Linux, while running it under MinGW/Msys yields Msys. If you run
1 uname -r will give you kernel release.
[Bioinfo] Extract data using NCBI E-utilities
Today I am going to introduce a powerful tool to retrieve data from NCBI – E-utilities. This is a REST API for NCBI databases. I used the API several years ago, but recently I picked it up again for my projects, so I think that this is a good opportunity to make some records for my future use as well as for internet users. So let’s start.
Introduction The use of the API has the following format:
[Linux] Input password automatically
In this post, I will introduce an approach to input password programatically, which is useful if a repeated command needs password.
Note: this approach is subject to the risk of exposing your passwords to others, so use it with caution.
Let’s use sudo as an example. Normally when you type
1 sudo ls It will prompt for a password if you set one.
However, if you type
[Windows] Get running processes using PowerShell
As a computational biologist, I may want to get the commands running in current system. This is pretty simple to achieve in Unix-like systems (using ps -ef or top command), but need some effort in Windows system. Today, I’d like to introduce two ways to get the running processes in using Windows PowerShell.
The first is get-process, which will list running processes, generating a table like the below:
Handles NPM(K) PM(K) WS(K) CPU(s) Id SI ProcessName 162 12 1660 5160 0.
[R] format paragraph output
When programming in R, one may print some messages such as usage information. When it comes, the base function strwrap() becomes very convenient. It can wrap strings into equal-length lines and add indentation/prefixes to lines. Here I will demonstrate some features.
First, let’s create a sample string by reading the first 5 lines of the ‘THANKS’ document in R documentation.
# read 5 lines from the 'THANKS' document
x <- paste(readLines(file.
[Bioinfo] Nextflow framework
Recently, I was introduced to an amazing pipeline-writing framework – nextflow. It has the following features:
it abstracts a pipeline, which can be written in any language and run on many computing platforms such as Linux Slurm, PBS, AWS, etc.
it is composed of many processes, the executing order of which is determined by the dependencies of the input and output channels of each process.
the nextflow language is extension of the Groovy programming language, which is a programming language for Java virtual machine.
[R] fit polynomial regression in R
In R, we can fit a polynomial model by combinative use two functions poly() and lm().
Setup
Let’s start with using the R internal data cars:
data(cars)
x<-cars$speed # use the speed as predictor
y<-cars$dist # use the dist as response
Fit the models
Now, let’s get the polynomials for the variable x using the degree 3:
x1<-poly(x, 3, raw=TRUE)
x2<-poly(x, 3, raw=FALSE)
# check the resulted polynomials
head(x)
## [1] 4 4 7 7 8 9
head(x1)
## 1 2 3
## [1,] 4 16 64
## [2,] 4 16 64
## [3,] 7 49 343
## [4,] 7 49 343
## [5,] 8 64 512
## [6,] 9 81 729
head(x2)
## 1 2 3
## [1,] -0.