usage: pyfgs <seq> [options]
🔗🐍⏭️ PyO3 bindings and Python interface to FragGeneScanRs,
a gene prediction model for short and error-prone reads.
Input options 💽:
seq Sequence file (or '-' for stdin)
-m, --model Sequence error model (default: complete)
- short1: Illumina sequencing reads with about 0.1% error rate
- short5: Illumina sequencing reads with about 0.5% error rate
- short10: Illumina sequencing reads with about 1% error rate
- sanger5: Sanger sequencing reads with about 0.5% error rate
- sanger10: Sanger sequencing reads with about 1% error rate
- pyro5: 454 pyrosequencing reads with about 0.5% error rate
- pyro10: 454 pyrosequencing reads with about 1% error rate
- pyro30: 454 pyrosequencing reads with about 3% error rate
- complete: Complete genomic sequences or short sequence reads without sequencing error
-r, --reads Force FASTQ parsing (Overrides auto-detection)
-w, --whole-genome Strict contiguous ORFs. Disables error-tolerant frameshift detection.
Output options ⚙️:
Provide a PATH to save to a file, or use the flag alone to print to stdout.
--faa [PATH] Output protein FASTA
--fna [PATH] Output nucleotide FASTA
--bed [PATH] Output BED6+1 format
--gff [PATH] Output GFF3 format
--vcf [PATH] Output VCF v4.2 format
Other options 🚧:
-t, --threads Number of threads (default: optimal)
-v, --version Print version and exit
-h, --help Print help and exit