Create a text info file for an Assembly Object.
This intended purpose of this App is to produce a downloadable TEXT file about an Assembly object.
Most KBase data objects already have some type of viewable HTML table, either as output from an App or by dragging the object onto the Narrative. This App serves a different purpose. This App creates data files that are downloadable and used with local tools such as Excel or informatic scripts.
This App creates files on the contents of an Assembly object. A Summary section has a preview of the full output. It is intended to be a preview of the downloadable file. If the file is tab or comma delimited, it may appear misaligned on the screen but readable by a computer script. The HTML link opens a new tab with the full output. The link for downloading the files is in the Files section of the output.
The inputs are:
- The KBase Assembly object (uploaded or output from an app)
- A checkbox for whether or not to include the FASTA of the Assembly object
The outputs are:
- A Link section with a link to the requested file that can be opened in another browser tab.
- One downloadable file in the Files section. The file has the following sections:
- The metadata of the Assembly object. This includes the length of the DNA sequence, the number of contigs, the fraction GC content, a taxon reference, and a FASTA handle reference.
- A count of the As, Cs, Gs, and Ts in the Assembly
- A list of the contigs in the Assembly
- Contig name (e.g., AKKW01000148)
- Length of the contig
- GC fraction of the contig
- Number of Ns
- Contig ID (can be the same as the name)
- Contig description from the FASTA header line
- OPTIONALLY: the DNA of the contigs in FASTA format.
- Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163 , https://www.nature.com/articles/nbt.4163
Module Commit: e9d2566b748fd735590f131da284ca44aaf5aefb