Sequence Composition: fast shell method Motivation This post was inspired to “verify” a Python Script meant to compute the sequence composition of amino acids, as suggested by ChatGPT. (See ChatGPT_Protein_Composition.ipynb, or viewer ChatGPT_Protein_Composition.ipynb.) The code …
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Magic-BLAST analysis of NextGen Reads
NCBI Magic-BLAST Workshop The intermediate level workshop Analyzing & Visualizing NextGen Reads with Magic-BLAST – [Archived] is designed for biologists who are comfortable working with the command-line (bash) and who are interested in performing some early …
PATH: the overlooked crucial variable
What is PATH There are many technical definitions that can be found, but in simple terms, PATH is a list of directories.The listed directories will contain the software that run on the computer, including the …
Understanding Python installation mess
Summary Useful ramblings about the difficulties to understand Python installation on macOS. In this Tutorial-like post we’ll see: – Where is Python installed, and which version – Upgrading to a new Python.org version, without replacement …
Accessing BOX on macOS with command line
UW personnel has access to Box, a cloud drive to store documents. While the older “Box Sync” application kept a copy of every file and folder on the local computer, the newer “box drive” …
Learn X in Y minutes
Learn X in Y minutes In the past we had “flash cards” to memorize and review materials. This site Learn X in Y minutes has one-page reminders that can be used to re-learn material or …
1to3 and 3to1 peptide sequence conversion
Summary 1. How to easily convert a string of character to appear one character per line> Either of: echo “abcdefg” | fold -w1 echo “abcdefg” | grep -o . 2. How to convert amino acid …
Reformat every other line with paste
Sometimes a very simple command can accomplish amazing tasks. Recently I had a list with alternating entries on every other line with about 200 lines, and lots of uneven text. But I wanted to …
PowerShell – an opinionated primer
PowerShell One day I discovered that there was a Windows App called “PowerShell” while searching on my Windows 10 installation. I did not pay much attention to it even if I stumbled upon it a …
csvkit command-line spreadsheet can convert and compute multiple Excel files
(Last edit: April 11, 2023) Summary csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. (csvkitis written in python.) csvkit Documentation: csvkit.rtfd.org csvkit Repository: …