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phanotate

PHANOTATE: a gene caller for phages.

https://github.com/deprekate/phanotate

Science Score: 26.0%

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  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
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    Academic publication links
  • ○
    Committers with academic emails
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.5%) to scientific vocabulary

Keywords

annotate-phage-genomes annotation genomics phage
Last synced: 6 months ago · JSON representation

Repository

PHANOTATE: a gene caller for phages.

Basic Info
  • Host: GitHub
  • Owner: deprekate
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 1.33 MB
Statistics
  • Stars: 78
  • Watchers: 9
  • Forks: 11
  • Open Issues: 12
  • Releases: 2
Topics
annotate-phage-genomes annotation genomics phage
Created almost 9 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License Citation

README.md

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

phiX174CDS[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

phiX174CDS[100..627] [note=score:-4.827981E+02] MFQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYFDSLTVNAGNGGFLHCIQMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESSSVPTTLPTAYDVYPLNGRHDGGYYTVKDCVTIDVLPRTPGNNVYVGFMVWSNFTATKCRGLVSLNQVIKEIICLQPLK*

Owner

  • Name: Katelyn
  • Login: deprekate
  • Kind: user
  • Location: San Diego, California

Super Scientist

GitHub Events

Total
  • Issues event: 4
  • Watch event: 9
  • Issue comment event: 9
  • Push event: 3
  • Fork event: 2
Last Year
  • Issues event: 4
  • Watch event: 9
  • Issue comment event: 9
  • Push event: 3
  • Fork event: 2

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 128
  • Total Committers: 2
  • Avg Commits per committer: 64.0
  • Development Distribution Score (DDS): 0.125
Past Year
  • Commits: 3
  • Committers: 1
  • Avg Commits per committer: 3.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
deprekate d****e@g****m 112
Robert Edwards r****s@g****m 16

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 26
  • Total pull requests: 16
  • Average time to close issues: 23 days
  • Average time to close pull requests: 26 days
  • Total issue authors: 21
  • Total pull request authors: 3
  • Average comments per issue: 4.5
  • Average comments per pull request: 0.06
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: 3 months
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 5.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • snayfach (3)
  • ilyavs (2)
  • linsalrob (2)
  • raw937 (2)
  • guille0387 (1)
  • dcampbdc (1)
  • pck0 (1)
  • songmj86 (1)
  • olsonanl (1)
  • telatin (1)
  • manuss11 (1)
  • aponsero (1)
  • noutin2020 (1)
  • jmeppley (1)
  • kshingler (1)
Pull Request Authors
  • deprekate (9)
  • linsalrob (6)
  • vloux (1)
Top Labels
Issue Labels
Pull Request Labels
enhancement (1)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 262 last-month
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 2
    (may contain duplicates)
  • Total versions: 17
  • Total maintainers: 2
pypi.org: phanotate

A a tool to annotate phage genomes

  • Versions: 16
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 262 Last month
Rankings
Dependent packages count: 7.3%
Stargazers count: 8.8%
Average: 11.6%
Dependent repos count: 11.8%
Forks count: 12.6%
Downloads: 17.4%
Maintainers (1)
deprekate
Last synced: 6 months ago
spack.io: py-phanotate

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.

  • Versions: 1
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Stargazers count: 21.7%
Average: 26.5%
Forks count: 27.0%
Dependent packages count: 57.3%
Maintainers (1)
adamjstewart
Last synced: 6 months ago

Dependencies

setup.py pypi
  • fastpath >=1.3