Inputs and Outputs
The only input is a path to a .fasta file that you want to analyze.
This file should include the genomic sequences of interest.
Once the analysis is complete, HIVIntact will generate four output files:
| Filename | Description |
|---|---|
| errors.json | This file contains associations between sequences and their identified defects. |
| orfs.json | This file contains associations between sequences and their identified Open Reading Frames (ORFs). |
| intact.fasta | This file contains a list of sequences with no fatal defects identified. These sequences are considered putative intact genomes. |
| nonintact.fasta | This file contains a list of sequences with identified defects. These sequences are not considered putative intact genomes. |
| blast.csv | This file contains output from BLASTN software. It is produced conditionally. |
If you pass the --output-csv option to HIVIntact, the output format will be .csv instead of .json.
Here is an example of the contents of the errors.csv file:
| sequence_name | error | message |
|---|---|---|
| KX505501.1 | DeletionInOrf | ORF pol at 2084-5096 can have maximum deletions 30, got 2892 |
| KX505501.1 | RevResponseElementDeletion | Query Sequence exceeds maximum deletion tolerance in RRE. Contains 35 deletions with max tolerance of 20 deletions. |
| MN691959 | InternalStopInOrf | Smaller ORF vpu at 6060-6309 contains an internal stop codon |
| MK114856.1 | APOBECHypermutationDetected | Query sequence shows evidence of APOBEC3F/G-mediated hypermutation (p = 3.639064030015132e-65). |
| MK116110.1 | PackagingSignalDeletion | Query Sequence exceeds maximum deletion tolerance in PSI. Contains 93 deletions with max tolerance of 10 deletions. |