tseemann / phastaf

Identify phage regions in bacterial genomes for masking purposes

⚠️ THIS SOFTWARE IS STILL IN VERY EARLY DEVELOPMENT!

phastaf

Identify phage regions in bacterial genomes for masking purposes

Introduction

Quick Start

% head -n 4 contigs.fna
>AE004092.2 Streptococcus pyogenes M1 GAS, complete genome
TTGTTGATATTCTGTTTTTTCTTTTTTAGTTTTCCACATGAAAAATAGTTGAAAACAATAGCGGTGTCCC
CTTAAAATGGCTTTTCCACAGGTTGTGGAGAACCCAAATTAACAGTGTTAATTTATTTTCCACAGGTTGT
GGAAAAACTAACTATTATCCATCGTTCTGTGGAAAACTAGAATAGTTTATGGTAGAATAGTTCTAGAATT

% phastaf --outdir out contigs.fna

% cat out/phage.bed
AE004092.2	529586	570503	370.1
AE004092.2	778519	821003	370.2
AE004092.2	1189119	1222648	370.3
AE004092.2	1773338	1786887	370.4

Installation

Homebrew

brew install brewsci/bio/phastaf  # COMING SOON
phastaf --check

Using Homebrew will install all the dependencies for you: Linux or MacOS

Conda

conda install -c bioconda phastaf  # COMING SOON
phastaf --check

Learn more about Bioconda.

Source

git clone https://github.com/tseemann/phastaf.git
./phastaf/bin/phastaf --help
./phastaf/bin/phastaf --check

You will need to install all the dependencies manually:

• diamond >= 0.9
• bedtools >= 2.0
• any2fasta >= 0.4
• sort (GNU or BSD)

Feedback

Please file questions, bugs or ideas to the Issue Tracker

License

GPLv3

Citation

Not published yet.

Authors

• Torsten Seemann
• Jake Lacey
• Sharif Shaaban
• Federica Palma
• Rebecca Ji Bengtsson
• Nabil-Fareed Alikhan
• Carlus Deneke

phastaf's Issues

How to create a new updated database

Hello, the PHASTER database has since grown I believe, could you point me in some direction where I could figure out how to create a new dmnd file from the db file supplied from phaster.ca?

Thank you

Archaeal genomes

Hi Torsten,

Can Phastaf be used on metagenomes and archaeal genomes?

Thanks!

Alan

bedtools merge bug?

Hi Torsten!

I just tried to give phastaf a quick spin via conda install -c bioconda phastaf but then ran into this:

... stuff happening ...

[phastaf] Running: (bedtools merge -i diamond.coords.bed -d 2000 -c 1 -o count > phage.bed) 2>&1 | sed 's/^/[bedtools] /' | tee -a phastaf.log
[bedtools]
[bedtools] *****
[bedtools] ***** ERROR: Requested column 1, but database file diamond.coords.bed only has fields 1 - 0.
[phastaf] Wrote: phage.bed
[phastaf] Walltime used: 0 min 7 sec
[phastaf] Found a bug in phastaf? Post it at https://github.com/tseemann/phastaf/issues
[phastaf] Done.

Any idea what could be the problem?

Error: Database was built with a different version of diamond as is incompatible.

Hi, I get this error whenever I try and run phastaf despite --check showing the following

Using any2fasta - /home/jmmans/.conda/envs/any2fasta/bin/any2fasta | any2fasta 0.4.2
[phastaf] Using bedtools - /usr/local/easybuild/software/BEDTools/2.25.0-intel-2016.u3/bin/bedtools | bedtools v2.25.0
[phastaf] Using diamond - /usr/local/easybuild/software/diamond/0.9.10/diamond | diamond version 0.9.10
[phastaf] Using sort - /usr/bin/sort | sort (GNU coreutils) 8.22

am I missing something? Cheers

Fourth column in phage.bed

What does the fourth column in phage.bed file indicate?

Add TRAVIS support