A collection of simple and self-contained utilities that could be of interest for anyone working with the serratus platform.
- simple, meaning that all the tools in here should do a single, concrete thing well and do that one thing only (following the UNIX philosophy); in a single source file, that is meant to be executed with a simple command line call
- self-contained, meaning that anything needed to run each of these scripts should be present in this repository
If your script is not simple (i.e. requires more than one file or is expected to grow in functionality in the future) it most likely deserves a dedicated repository in serratus-bio.
All scripts should implement a --help argument that prints out detailed usage information with all the arguments it accepts and an explanation of what they do.
All scripts should exit with a 0 status code if nothing goes wrong, otherwise they should return a non-zero status code. Main output should go to stdout, while warnings and errors should go to stderr. Furthermore, design these scripts while keeping in mind that they could (and should) be used in a larger pipeline on a UNIX-like environment.
For each of the scripts listed below, a small sentence about what it does, a one-line sample usage with the most common use case as well as sample output from it should be provided.
Scripts that extract info from SRA or its related projects (like STAT). So far, we only have one script that uses node to run, so make sure you cd into this directory and run npm install to make sure it's good to go.
Returns all SRA/STAT taxonomy information found for a specific SRA run id.
Example
node stat-query-by-sra-id.js --depth=2 ERR2756788
Queries SRA/STAT for matches found on "Frank the Bat" (SRA ID: ERR2756788).
Remove the --depth argument to print out the full hierarchy of hits.
The output corresponds to the same data found on the "Analysis" tab on the NCBI Trace page for this entry.
Sample Output
STAT FOR SRA ID: ERR2756788
IDENTIFIED UNIDENTIFIED TOTAL
8,244,850 46.42% 9,515,859 53.58% 17,760,709 100.00%
cellular organisms [131567] 8,242,597 46.41%
Eukaryota [2759] 6,242,055 35.15%
Opisthokonta [33154] 6,224,366 35.05%
Viridiplantae [33090] 1,544 <0.01%
Amoebozoa [554915] 23 <0.01%
Euglenozoa [33682] 11 <0.01%
Alveolata [33630] 2 <0.01%
Bacteria [2] 1,989,553 11.20%
Proteobacteria [1224] 1,119,286 6.30%
Terrabacteria group [1783272] 623,179 3.51%
FCB group [1783270] 4,656 <0.01%
PVC group [1783257] 4,458 <0.01%
...