Useful diff Aliases

Add the following aliases to your ‘~/.bashrc’ for some diff goodness: alias diff-side-by-side='diff --side-by-side -W"`tput cols`"' alias diff-side-by-side-changes='diff --side-by-side --suppress-common-lines -W"`tput cols`"' You can, of course, use shorter alias names in good old UNIX tradition, e.g. ‘ssdiff’ and ‘sscdiff’. You might be wondering why (a) I did not do so, and (b) what is the point, conversely, of having aliases that are almost as long as the commands that they are aliasing.

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Setting Up Git to Use Your Diff Viewer or Editor of Choice

Git offers two ways of viewing differences between commits, or between commits and your working tree: diff and difftool. The first of these, by default, dumps the results to the standard output. This mode of presentation is great for quick summaries of small sets of changes, but is a little cumbersome if there are a large number of changes between the two commits being compared and/or you want to closely examine the changes, browsing back-and-forth between different files/lines, search for specific text, fold away or hide non-changed lines etc.

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Using DendroPy Interoperability Modules to Download, Align, and Estimate a Tree from GenBank Sequences

The following example shows how easy it can be to use the three interoperability modules provided by the DendroPy Phylogenetic Computing Library to download nucleotide sequences from GenBank, align them using MUSCLE, and estimate a maximum-likelihood tree using RAxML. The automatic label composition option of the DendroPy genbank module creates practical taxon labels out the original data. We also pass in additional arguments to RAxML to request that the tree search be carried out 250 times (['-N', '250']).

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Vim Regular Expression Special Characters: To Escape or Not To Escape

Vim’s regular expression dialect is distinct from many of the other more popular ones out there today (and actually predates them). One of the dialect differences that always leaves me fumbling has to do with which special characters need to be escaped. Vim does have a special “very magic” mode (that is activated by “\v” in the regular expression) that makes thing very clean and simple in this regard: only letters, numbers and underscores are treated as literals without escaping.

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Unconditionally Accepting All Merging-In Changes During a Git Merge

Merge conflicts suck. It is not uncommon, however, that you often just know that you really just want to accept all the changes from the branch that you are merging in. Which makes things a lot simpler conceptually. The Git documentation suggests that this can also be procedurally simple as well, as it mentions the “-s theirs” merge strategy which does just that, i.e., unconditionally accept everything from the branch that you are merging in:

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The Power and Precision of Vim's Text Objects: Efficent, Elegant, Awesome.

Vim’s text objects are not only a powerful, flexible and precise way to specify a region of text, but also intuitive and efficient. They can be used with any command that can be combined with a motion (e.g., “d”, “y”, “v”, “r”), but in this post I will be using the “c” command (“change”) to illustrate them. Imagine you were on a line looked like this, with the cursor on the letter “r” of the word “dry”:

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Supplementary Command-History Logging in Bash: Tracking Working Directory, Dates, Times, etc.

Introduction Here is a way to create a secondary shell history log (i.e., one that supplements the primary “~/.bash_history”) that tracks a range of other information, such as the working directory, hostname, time and date etc. Using the “HISTTIMEFORMAT” variable, it is in fact possible to store the time and date with the primary history, but the storing of the other information is not as readibly do-able. Here, I present an approach based on this excellent post on StackOverflow.

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Stripping Paths from Files in TAR Archives

There is no way to get tar to ignore directory paths of files that it is archiving. So, for example, if you have a large number of files scattered about in subdirectories, there is no way to tell tar to archive all the files while ignoring their subdirectories, such that when unpacking the archive you extract all the files to the same location. You can, however, tell tar to strip a fixed number of elements from the full (relative) path to the file when extracting using the “--strip-components” option.

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Pure-Python Implementation of Fisher's Exact Test for a 2x2 Contingency Table

While Python comes with many “batteries included”, many others are not. Luckily, thanks to generosity and hard work of various members of the Python community, there are a number of third-party implementations to fill in this gap. For example, Fisher’s exact test is not part of the standard library. While Python comes with many “batteries included”, many others are not. Luckily, thanks to generosity and hard work of various members of the Python community, there are a number of third-party implementations to fill in this gap.

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Piping Output Over a Secure Shell (SSH) Connection

We all know about using scp to transfer files over a secure shell connection. It works fine, but there are many cases where alternate modalities of usage are required, for example, when dealing when you want to transfer the output of one program directly to be stored on a remote machine. Here are some ways of going about doing this. Let “$PROG” be a program that writes data to the standard output stream.

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