vegah/Fantasista.DNAv0.0.5
.NET 8.0
Tooling for parsing different biology formats. Currently supporting Vcf files Sam files Gff3 files Fasta files Fastq files Human Genome Variation Society (HGVS) format
Get Started
$ dotnet add package Fantasista.DNAReadme
Fantasista.DNA
A library for reading, handling and working with bioinformatic files and formats.
The library is work in progress, and it is mainly created to be able to work with this stuff myself.
Install
$ dotnet add package Fantasista.DNA
Roadmap
The first versions will prioritize reading different kinds of file formats. See list below over supported files.
Next versions:
- More tooling for alignments in sam files
- Reading Cram files
- Reading Bam files
Documentation
Examples
Complete API Documentation
Supported file formats:
| File format | Class | Description |
|---|---|---|
| Variant Call Format (VCF) | VcfStreamReader | Reads variations between reference genomes and sequences aligned to it |
| FASTA | FastaStreamReader | Reads the sequence format FASTA |
| FASTQ | FastqStreamReader | Reads the sequence format FASTQ |
| SAM | SamStreamReader | Reads SAM Files |
| Gff3 | Gff3StreamReader | Reads Gff3 Files |
Other supported parses
| Type | Class | Description |
|---|---|---|
| HGVS | HgvsVariant | Human Genome Variation Society Formatting iternationally-recognized standard for the description of DNA, RNA, and protein sequence variants. |
I found a bug
Please use Github Issues, or even better, fix it yourself and create a pull request. If you leave a bug issue, please add as much information as possible to make it easy to recreate the bug.
Where to find data
Are you new to bioinformatics?
There are a lot of places to find data files you could use for starting in bioinformatics.
- The ftp server at ClinVar
- Uniprot have a Download page