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. Then:

The following code snippet will return the mode(s) of a list of values, using the specified bin size. If "bin_size" is set to "None", then values are not binned.

The following code snippet is useful to "pretty-print" a tuple of dictionaries as a plain text table.

This paper describes how Google works.

The following script takes a space separated list of GenBank numbers as input, and then uses BioPython to download the corresponding sequences from GenBank, strips off all non-coding nucleotides, gives the sequences sensible names, and assembles them into a FASTA file.

msBayes is a suite of tools that support a Approximate Bayesian Computation approach for phylogeographic analysis, estimation and hypothesis testing.

msBayes is a suite of tools that support a Approximate Bayesian Computation approach for phylogeographic analysis, estimation and hypothesis testing. The following Python script can be used to ensure that various data files produced by programs in the msBayes pipeline all have the same number and type of columns.

Things to note regarding the operation of the script:

Have you ever encountered an "Argument list too long" error? For example:

I find this a pretty useful wrapper around SGE"s "qstat". Enhancements include much more compact representation of useful information (e.g., excludes "department"), and also allows sorting (or reverse sorting) by any one of the display columns:

Deleting a local tag is straightforward, and uses the "git tag":

# git tag -d v.7b

Deleting a remote tag is the same syntax and idiom (and, in fact, command) as deleting a remote branch:

# git push origin :v.7b