My software CUA is cited by a Cell Reports paper
Very exciting: my software CUA is cited by a paper published at Cell Reports. This is very encouraging for me to further improve the software.
My paper describes the software was published at BioRxiv. You can also find documentation (including a tutorial) at CPAN.
Recently, more and more studies show that codon usage is, in addition to translation, relevant to mRNA stability, transcription, etc, making the observation of codon usage bias in many genomes more mysterious.
[Python] Parse command arguments with orgparse
Parsing command-line arguments is common in programming. In Bash, one can use getopts. In Perl, one can use the module Getopt::Long. In Python, we can use the package argparse.
The major steps of using the package include 3 steps:
Create a parser.
Add arguments.
Parse the arguments.
Here I will describe each step in details, particularly the options of the functions.
Create a parser
Below is a simple example of creating a parser object.
WSL -- a perfect replacement of Cygwin and Mingw
As a program developer, I love working on the command of Linux for its richment in convenient tools, such as sed, awk, grep, vi, etc.
Every time when I bought a new windows computer, I would install cygwin or MinGW for using these linux tools. With windows 10 (version Fall Creators update or later), one can install Windows Subsystem for Linux (WSL) in windows 10 from store, just like installing an app.
Can we put genes in one chromosome?
Organisms often have more than one chromosomes to carry their genetic materials such as genes. For example, a human individual has 23 pairs of different chromosomes, and a baking yeast Saccharomyces cerevisiae has 16 different chromosomes when in haploid status.
Why do an organism have many chromosomes other than one? Particularly, if one thinks that only genes on chromosomes are useful and the rest may be junk, he may think that putting all genes in a chromosome will be completely fine and this is more efficient in saving energy of synthesizing “useless” portions of chromosomes.
Science without (applying for) funds
Nowdays, scientific research is often done at institutions such as universities and companies.
A fact is that research often costs a lot of money and research results mostly don’t generate profit. Therefore, researchers often suffer the lack of research funds, especially recent years.
I often ponder how research can be sustainable and whether one can do research with applying for funds.
I happened to find Dr. Robert C. Edgar’s web page today when I search literature.
Blog with "blogdown"
I am very excited that I can start writing blogs with Markdown (even better, Rmarkdown), and then push the posts to GitHub. Then done!! The posts will show up at https://zhenguozhang.zone/ hosted at https://netlify.com. I don’t need worry deployment of the website.
For this to work, I used the excellent R package blogdown, written by the R celebrity Yihui Xie. Since the process is so amazing, I would like to share it with you, so you can also benefit from it.
First post with blogdown
This is the first post I created with the R package blogdown.
Very excited!!!
Watch my coming posts.
Have a great day.
A Plain Markdown Post
This is a post written in plain Markdown (*.md) instead of R Markdown (*.Rmd). The major differences are:
You cannot run any R code in a plain Markdown document, whereas in an R Markdown document, you can embed R code chunks (```{r}); A plain Markdown post is rendered through Blackfriday, and an R Markdown document is compiled by rmarkdown and Pandoc. There are many differences in syntax between Blackfriday’s Markdown and Pandoc’s Markdown.
Hello R Markdown
R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.
You can embed an R code chunk like this:
summary(cars)
## speed dist ## Min. : 4.0 Min. : 2.00 ## 1st Qu.:12.0 1st Qu.: 26.00 ## Median :15.0 Median : 36.00 ## Mean :15.4 Mean : 42.98 ## 3rd Qu.
Lorem Ipsum
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.