tinyRNA provides an all-in-one solution for precision analysis of sRNA-seq data. At the core of tinyRNA is a highly flexible counting utility, tiny-count, that allows for hierarchical assignment of reads to features based on positional information, extent of feature overlap, 5’ nucleotide, length, and strandedness.
When this argument is provided, tiny-count simply copies the Paths File, Samples Sheet, and Features Sheet to the current directory and exits, ignoring all other arguments
--get-templates cannot be used in combination with the --paths-file argument
I had originally intended get-templates (sans leading dashes), but this was surprisingly difficult to accomplish without a lot of hacking in argparse, so this was the cleaner and more reliable solution
Misc. improvements to the tiny-count helpstring
The --out-prefix argument is now optional. This had to be done to allow a mutually exclusive required group between --get-templates and --paths-file. Its default value is "tiny-count_{timestamp}". The "{timestamp}" token is replaced with the current date/time. Users can also use this token in their own prefix
Default argument values are now indicated at the end of each argument's help string
A more succinct intro description that doesn't mention tinyRNA's recount/replot option
The --help and --all-features arguments are now hidden from the helpstring (and the entry for All Features has been removed from the documentation)
Configuration file changes
Files in the /tiny/templates directory no longer contain an example configuration. The old contents have been moved to /tests/testdata because they are utilized in some unit tests
The Input FASTQ Files header has been renamed to FASTQ/SAM Files in the Samples Sheet
Misc changes
The command tiny get-template has been corrected to tiny get-templates (plural)
Shortened the introductory sections in tiny-count.md and corrected outdated info in the standalone section. Removed the warning about reusing the same prefix between standalone runs since the default prefix and {timestamp} token should make this a non issue. Also moved the selection diagram down so that it is right before the Stage 1 section.
--get-templates
--get-templates
cannot be used in combination with the--paths-file
argumentget-templates
(sans leading dashes), but this was surprisingly difficult to accomplish without a lot of hacking in argparse, so this was the cleaner and more reliable solutionMisc. improvements to the tiny-count helpstring
--out-prefix
argument is now optional. This had to be done to allow a mutually exclusive required group between--get-templates
and--paths-file
. Its default value is "tiny-count_{timestamp}". The "{timestamp}" token is replaced with the current date/time. Users can also use this token in their own prefix--help
and--all-features
arguments are now hidden from the helpstring (and the entry for All Features has been removed from the documentation)Configuration file changes
Input FASTQ Files
header has been renamed toFASTQ/SAM Files
in the Samples SheetMisc changes
tiny get-template
has been corrected totiny get-templates
(plural)