Adds an applet, ngs-viral-fasta-fetcher, to the ngs-viral project. This applet is a wrapper around the ncbi.py fetch_fastas_and_feature_tables function to fetch and combine fasta files from Genbank. This applet is meant to be used by users of the viral-ngs pipeline who want to work on assemblies beyond the Ebola and Lassa viruses.
Original request from Danny:
...... as long as we have a small applet available for folks to fetch and build their own database for some other virus than Lassa or Ebola. Folks have noticed a number of other interesting viruses in our sequence data (GB virus C, Orungyo, etc) and the underlying code should be able to assemble those just fine as well.
The applet is built by build_workflow.py into the main target folder (not in the applet folder) so that it is directly visible to users.
@alphabdiallo cc @mlin
Adds an applet,
ngs-viral-fasta-fetcher, to the ngs-viral project. This applet is a wrapper around thencbi.py fetch_fastas_and_feature_tablesfunction to fetch and combine fasta files from Genbank. This applet is meant to be used by users of the viral-ngs pipeline who want to work on assemblies beyond the Ebola and Lassa viruses.Original request from Danny: ...... as long as we have a small applet available for folks to fetch and build their own database for some other virus than Lassa or Ebola. Folks have noticed a number of other interesting viruses in our sequence data (GB virus C, Orungyo, etc) and the underlying code should be able to assemble those just fine as well.
The applet is built by
build_workflow.pyinto the main target folder (not in theappletfolder) so that it is directly visible to users.File structure and built applet: example built applet
Run: example usage
TODO: Document this applet and its use case in wiki page.