This command is mostly used to load the reference genome. The reference sequences are exclusively used to feed JBrowse.
If the reference sequences are really long (>200Mbp), there may be memory issues during the loading process and JBrowse may take too long to render the tracks. To avoid that, it's possible to use the parameter (--nosequence) and configure JBrowse to get the reference data from a FASTA file.
python manage.py load_fasta --file organism_chrs.fa --soterm chromosome --organism 'Arabidopsis thaliana'- Loading this file can be faster if you increase the number of threads (--cpu).
python manage.py load_fasta --help| --file | FASTA File * |
| --organism | Species name (eg. Homo sapiens, Mus musculus) * |
| --soterm | SO Sequence Ontology Term (eg. chromosome, assembly) * |
| --description | Description |
| --url | URL |
| --doi | DOI of a reference stored using load_publication (eg. 10.1111/s12122-012-1313-4) |
| --nosequence | Don't load the sequences |
| --cpu | Number of threads |
* required fields
If, by any reason, you need to remove a fasta dataset you should use the command remove_file. If you delete a file, every record that depend on it will be deleted on cascade.
python manage.py remove_file --help- This command requires the file name (Dbxrefprop.value)