VPrimer: A method of designing and updating primer and probe with high variant coverage for RNA virus detection
https://pubmed.ncbi.nlm.nih.gov/34951850/
https://github.com/qhtjrmin/VPrimer/
To get VPrimer input data generator, follow the queries.
$ git clone https://github.com/Hajin-Jeon/VPrimer-input-generator
The source codes are in "src" folder.
The guidline for execution is in section 2.
VPrimer input data generator needs the following software to run in the system:
- gcc/g++ 4.8.x or later
The example of input files that can be used are in "input_test" folder.
The required data is as follow in "FASTA" folder:
- host sequence (host.fasta, in FASTA format)
- virus sequence (virus.fasta, in FASTA format)
At this time, the format of the virus sequence should be as follows:
- starts with '>' sign
- each column must be separated by the '|' symbol
- The structure as "(Coding Sequence) [Virus Name]"
- (for example: >QLI57642.1 |hypothetical protein [Orf virus]): starts with '>' sign, separated by '|' symbol, CDS is hypothetical protein, and virus name is Orf virus
input "make" in the "src" folder. Then, the file "VPrimer_input_generator" would be generated.
The basic execution order is as follows.
- host sequence parsing
- virus sequence parsing
- generating mapping data
Optional arguments:
| Parameter | Default | Description |
|---|---|---|
| -i | ../FASTA | input FASTA sequence folder path |
| -d | ../data | final output folder path |
| -o | ../result | intermediate data folder path |
| -h (or others) | (none) | help message |
Example:
./VPrimer_input_generator -i /home/(username)/VPrimer/FASTA -d /home/(username)/VPrimer/data/ -o /home/(username)/VPrimer/result/
The intermediate data will be generated as follow in "data" folder:
- mapping data for sid and sequence (virus_sid_sequence.txt)
- mapping data for tid and sequence (host_tid_sequence.txt, virus_tid_sequence.txt)
- virus_sid_tids.txt
- virus_annotation_sid.txt
- virus_tid_acc.txt
- virus_sid_accs.txt
- virus_virus_oid.txt
- virus_viruscds_cid.txt
- virus_sid_oids.txt
- virus_oid_sid.txt
- virus_sid_cids.txt
- virus_cid_sid.txt
- virus_sort_tid_vidcds_seq.txt
- virus_sort_tid_cid.txt
- virus_sort_annotation_sid.txt
- virus_sort_oid_tids.txt
- virus_sort_tid_oid.txt
- virus_sort_tid_vids.txt
- virus_sort_oid_vids.txt
- virus_sort_vid_acc.txt
The result data will be generated as follow in "result" folder:
- mapping data for sid and sequence (host_sid_sequence, virus_sort_tid_seq.txt)
- mapping data for virus sequence (oid-vidset, sid-oid, sid-vidset)
- annotation data (host_annotation.txt, virus_sort_annotation_sid.txt) (not be used in VPrimer CLI mode)
If you have any question, please contact [email protected]