Skip to main content

A a tool to annotate phage genomes

Project description

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

 git clone https://github.com/deprekate/PHANOTATE.git
 pip3 install PHANOTATE/.

PHANOTATE Example

Run on included sample data:

phanotate.py tests/NC_001416.1.fasta 

Output is the predicted ORFs, and should look like

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:

$ 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:

$ 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:

$ phanotate.py tests/phiX174.fasta -f faa | head -n2
>phiX174_CDS_[100..627] [note=score:-4.827981E+02]
MFQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYFDSLTVNAGNGGFLHCIQMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESSSVPTTLPTAYDVYPLNGRHDGGYYTVKDCVTIDVLPRTPGNNVYVGFMVWSNFTATKCRGLVSLNQVIKEIICLQPLK*

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

phanotate-1.6.7.tar.gz (114.3 kB view details)

Uploaded Source

Built Distribution

phanotate-1.6.7-py2.py3-none-any.whl (31.0 kB view details)

Uploaded Python 2Python 3

File details

Details for the file phanotate-1.6.7.tar.gz.

File metadata

  • Download URL: phanotate-1.6.7.tar.gz
  • Upload date:
  • Size: 114.3 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.9.17

File hashes

Hashes for phanotate-1.6.7.tar.gz
Algorithm Hash digest
SHA256 81889ccaa04bd530a7f2f0b93064c748940b573d736c824f2e97450df5b2033e
MD5 5c3b845f98a3766b2c5293ffbecc58d0
BLAKE2b-256 f285d30456168ba839c9cd97ea241e245fef7d6cbdeaa931504c51447f0dd9a1

See more details on using hashes here.

File details

Details for the file phanotate-1.6.7-py2.py3-none-any.whl.

File metadata

  • Download URL: phanotate-1.6.7-py2.py3-none-any.whl
  • Upload date:
  • Size: 31.0 kB
  • Tags: Python 2, Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.9.17

File hashes

Hashes for phanotate-1.6.7-py2.py3-none-any.whl
Algorithm Hash digest
SHA256 f7072f5ffda3fcbfabb56329c6ae511abc5f2a86252bd0e72e6d06d6c64d00d5
MD5 9255e7580e5e8fe942177392c246552b
BLAKE2b-256 85a2d036dfd85817dae30eaf6a56ee0bfc090d2dbc46e62252b3fa61ed3c17b5

See more details on using hashes here.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page