Introduction
------------
PHANOTATE is a tool to annotate phage genomes. It uses the assumption that non-coding
bases in a phage genome is disadvantageous, and then populates a weighted graph to
find the optimal path through the six frames of the DNA where open reading frames
are beneficial paths, while gaps and overlaps are penalized paths.
To install `PHANOTATE`,
```
pip3 install phanotate
```
or
```sh
git clone https://github.com/deprekate/PHANOTATE.git
pip3 install PHANOTATE/.
```
PHANOTATE Example
--------------
Run on included sample data:
```sh
phanotate.py tests/NC_001416.1.fasta
```
Output is the predicted ORFs, and should look like
```sh
125 187 +
191 736 +
741 2636 +
2633 2839 +
2836 4437 +
4319 5737 +
...
```
`PHANOTATE` has the ability to output different formats: genbank, gff, gff3, fasta
Output a genbank file that contains the genes and genome:
```sh
$ phanotate.py tests/phiX174.fasta -f genbank | head
LOCUS phiX174 5386 bp
FEATURES Location/Qualifiers
CDS 100..627
/note=score:-4.827981E+02
CDS 687..1622
/note=score:-4.857517E+06
CDS 1686..3227
/note=score:-3.785434E+10
CDS 3224..3484
/note=score:-3.779878E+02
```
Output the nucleotide bases of the gene calls in fasta format:
```sh
$ phanotate.py tests/phiX174.fasta -f fna | head -n2
>phiX174_CDS_[100..627] [note=score:-4.827981E+02]
atgtttcagacttttatttctcgccataattcaaactttttttctgataagctggttctcacttctgttactccagcttcttcggcacctgttttacagacacctaaagctacatcgtcaacgttatattttgatagtttgacggttaatgctggtaatggtggttttcttcattgcattcagatggatacatctgtcaacgccgctaatcaggttgtttctgttggtgctgatattgcttttgatgccgaccctaaattttttgcctgtttggttcgctttgagtcttcttcggttccgactaccctcccgactgcctatgatgtttatcctttgaatggtcgccatgatggtggttattataccgtcaaggactgtgtgactattgacgtccttccccgtacgccgggcaataacgtttatgttggtttcatggtttggtctaactttaccgctactaaatgccgcggattggtttcgctgaatcaggttattaaagagattatttgtctccagccacttaagtga
```
Output the amino-acids of the gene calls in fasta format:
```sh
$ phanotate.py tests/phiX174.fasta -f faa | head -n2
>phiX174_CDS_[100..627] [note=score:-4.827981E+02]
MFQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYFDSLTVNAGNGGFLHCIQMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESSSVPTTLPTAYDVYPLNGRHDGGYYTVKDCVTIDVLPRTPGNNVYVGFMVWSNFTATKCRGLVSLNQVIKEIICLQPLK*
Raw data
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