orf-finder

Nucleic-acid metrics and six-frame open reading frame scanning from the command line. Pure Python with no third-party dependencies, and a self-contained HTML report that opens from a local disk without a network connection.

Install

Install the prerelease from PyPI:

python -m pip install --pre norvara-orf-finder

The Python package and command keep the shorter project name:

import orf_finder

orf-finder --version

Quickstart

orf-finder scan --input examples/phix174.fasta --min-length 300 --report phix174.html

> NC_001422.1  Escherichia phage phiX174, complete genome
  5,386 nt DNA  A=1,291 T=1,684 C=1,157 G=1,254 N=0  GC=44.76%  mass=1,663,975.55 g/mol
  8 ORFs
    ORF      FRAME       START         END       NT      AA  START STOP  
    ORF1        +2       1,001       2,284    1,284     427  ATG   TGA   
    ORF2        +3       2,931       3,917      987     328  ATG   TAA   
    ORF3        +1       3,076       3,684      609     202  ATG   TGA   
    ORF4        -1       1,094       1,651      558     185  ATG   TGA   
    ORF5        +1       2,395       2,922      528     175  ATG   TGA   
    ORF6        +3         390         848      459     152  ATG   TAA   
    ORF7        -1       1,772       2,167      396     131  ATG   TAA   
    ORF8        +1       3,946       4,263      318     105  ATG   TAA   

The report adds the full composition breakdown, a per-frame ORF census, the coordinate table and every translated peptide.

Options

-i, --input PATH         FASTA file to scan, or '-' for standard input
-m, --min-length N       smallest ORF to report, in nucleotides
                         including the stop codon (default: 300)
-g, --table TABLE        genetic code by number, name or alias
                         (default: 1, the standard code)
-b, --begin N            first base of the fragment to scan (default: 1)
-e, --end N              last base of the fragment; 0 means to the end
    --strand {both,plus,minus}
    --start-codons       atg | alt | any | an explicit comma-separated list
-n, --ignore-nested      drop ORFs completely placed within a longer ORF
                         on the same strand
    --include-truncated  also report an ORF that reaches the end of the
                         sequence without a stop codon
    --no-peptides        omit peptide sequences from the HTML report

orf-finder tables lists the 27 bundled genetic codes.

Outputs

Any combination may be requested in a single pass; the sequence is scanned once. Feature-table output requires unique identifiers in the input FASTA, so its sequence names match the source. For a nonstandard genetic code, each CDS carries the selected transl_table qualifier.

Reading the output

• Coordinates are 1-based and inclusive on the forward strand, with start <= end on both strands; a minus-strand ORF is read from end towards start.
• Frames +1, +2, +3 are offsets into the sequence as given; -1, -2, -3 are offsets into its reverse complement.
• length_nt includes the stop codon and --min-length filters on it; length_aa is the peptide, which excludes it.
• With --start-codons atg or alt, one ORF is reported per in-frame stop codon, beginning at the 5'-most start codon after the preceding stop, and an initiation codon is translated as methionine. With any, every region between two stops is an ORF and the first region of a frame is marked five_prime_partial, having no upstream stop. These regions have no required initiation codon; has_initiation_codon is false and feature-table/CDS FASTA outputs mark their 5' ends as partial.
• An explicitly listed start codon that the selected genetic code does not recognise as an initiator is still scanned, but retains its ordinary amino acid and is marked 5' partial.
• truncated marks an ORF that reaches the end of the sequence without a stop codon.
• GC content is computed over unambiguous bases; mass is approximate when ambiguity codes are present. RNA input is detected when U is present and T is absent, and is translated through the same table.

Genetic codes

All 27 translation tables are bundled, transcribed verbatim from the ncbieaa and sncbieaa strings of gc.prt, whose sha256 is recorded in genetic_code.py. Each table carries its own stop codons and its own initiation codons, so --start-codons alt means something different under each one:

orf-finder scan -i genome.fasta --table 11             # bacterial
orf-finder scan -i mito.fasta  --table vertebrate-mito # table 2

Limitations

• Sequences are treated as linear, so a feature crossing the origin of a circular molecule is not found.
• Alignment gaps are accepted but not removed, so a gapped sequence yields coordinates in alignment space and X residues where the gaps fall. Gaps contribute to length but are excluded from base composition and mass.
• The whole sequence is held in memory, which suits genes, plasmids, viruses and bacterial chromosomes rather than vertebrate chromosomes.
• An ORF is a reading frame, not a gene. No coding potential, ribosome binding site, splice site or homology evidence is considered.

Development

pip install -e ".[dev]"
pytest -q
python -m pyflakes src/orf_finder tests

License

Licensed under the PolyForm Noncommercial License 1.0.0. See LICENSE for the complete terms.