PATRIC families are somehow organized sets proteins that are related. Sometimes we want to get all the protein sequences in the family. Here’s how to do that using the PATRIC command line
Category Archives: Lab blog
Submitting a PATRIC genome annotation using the command line
The PATRIC BRC has a great command line interface that allows you to access much of the data remotely. Here is a simple recipe to submit a genome for annotation.
Teaching Bioinformatics
We teach a lot of bioinformatics. Here are some public resources we rely on. These are pulled from twitter, the web, and all over the place, and the text ended up being used elsewhere. Please feel free to suggest more to Rob!
Ulcerative Colitis, Crohn’s Disease, and Controls – Using Machine Learning to Identify the Key Bacterial Species
fastq-pair data sets
We recently released our new fastq-pair code that allows you to synchronize fastq files that are out of order. Here are some more data sets that you can use to test out fastq-pair.
Linux security tips and tricks
So you want to allow users to upload files to your server? This can be dangerous, very quickly someone will upload a malicious PHP script that allows them access to the directories of your web applications.
Here are some tips and tricks to aid in the safety of your server. We use all of these, and some others that are not included here so that the bad guys can’t figure out all of our security approaches!
Asking For Letters of Recommendation
At some point you will want to request a letter of recommendation from one of your Professors. Here are some tips that you should consider before you do so.
[source: the original idea was on a poster I saw at Tulsa Community College, Oklahoma, but I have added advice from others too]
Reading and writing to the same file
If you try to modify a file (removing all empty lines for example) using a command like:
cat file.txt | sed '/^$/d' > file.txt
you will end up with and empty file.txt. The reason is that bash parses the command line looking for “metacharacters” ( “|” , “>” and “space” in this case) that separate words, then groups and executes those words according to their precedence. This means that “> file.txt” get executed FIRST. This creates an empty file.txt (overwriting any existing file) and a “process” to redirect standard output to that file. Then “cat file.txt” get executed, but by now file.txt is empty. So “cat file.txt” outputs 0 lines, “sed ‘/^$/d’ ” deletes all 0 empty lines, and 0 lines get written to file.txt . This works as “intended” and bash outputs no error.
You can get around this using a temporal file.
cat file.txt | sed '/^$/d' > tmp_file.txt mv tmp_file.txt file.txt
But, as file.txt is technically a new file you might lose some information, in particular permissions and whether file.txt was originally a symbolic link or not.
Other options is to use sponge, which is part of moreutils and sadly not standard in many systems.
cat file.txt | sed '/^$/d' | sponge file.txt
SoCal Hackathon 2018
We are pleased to announce the SoCal Bioinformatics Hackathon.
From 10-12 January, 2018, the NCBI will help run a bioinformatics hackathon in Southern California hosted by San Diego State University! The hackathon will focus on advanced bioinformatics analysis of next generation sequencing data, proteomics, and metadata. This event is for researchers, including students and postdocs, who have already engaged in the use of bioinformatics data or in the development of pipelines for bioinformatics analyses from high-throughput experiments. Some projects are available to other non-scientific developers, mathematicians, or librarians.
Alpha, Beta, and Gamma diversity with ice cream
Sitting in a master-class on ecology from Jennifer Martiny at UCI someone asked if you could explain ecological diversity in terms of ice cream. Of course you can.