dnaapler 0.1.0__tar.gz

dnaapler-0.1.0/HISTORY.md

@@ -0,0 +1,20 @@
+=======
+History
+=======
+
+0.1.0 (2022-10-12)
+------------------
+
+* Completely overhauled
+* First stable released with pypi and conda 
+* `plassembler chromosome` added
+* `plassembler custom` added
+* `plassembler mystery` added 
+* `plassembler phage` added
+* `plassembler plasmid` added
+
+
+0.0.1 (2022-10-12)
+------------------
+
+* First release (conda only `conda install -c gbouras dnaapler`)

dnaapler-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2021, George Bouras
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

dnaapler-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: dnaapler
+Version: 0.1.0
+Summary: Reorients assembled microbial sequences
+Home-page: https://github.com/gbouras13/dnaapler
+License: MIT
+Keywords: microbial,bioinformatics
+Author: George Bouras
+Author-email: george.bouras@adelaide.edu.au
+Requires-Python: >=3.8,<4.0
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Dist: biopython (>=1.76)
+Requires-Dist: click (>=8.0.0)
+Requires-Dist: loguru (>=0.5.3)
+Requires-Dist: pandas (>=1.4.2)
+Requires-Dist: pyrodigal (>=2.0.0)
+Requires-Dist: pyyaml (>=6.0)
+Project-URL: Repository, https://github.com/gbouras13/dnaapler
+Description-Content-Type: text/markdown
+
+[![CI](https://github.com/gbouras13/dnaapler/actions/workflows/ci.yaml/badge.svg)](https://github.com/gbouras13/dnaapler/actions/workflows/ci.yaml)
+[![codecov](https://codecov.io/gh/gbouras13/dnaapler/branch/refactor/graph/badge.svg?token=4B1T2PGM9V)](https://codecov.io/gh/gbouras13/dnaapler)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+
+# dnaapler
+
+Description
+----------
+
+`dnaapler` is a simple python program that takes a single nucleotide input sequence (in FASTA format), finds the desired start gene using `blastx` against an amino acid database, checks that the start of a gene is found, and if so, then reorients the chromosome to begin with this genes on the forward strand. 
+
+It was designed to replicate the reorientation functionality of [Unicycler](https://github.com/rrwick/Unicycler/blob/main/unicycler/gene_data/repA.fasta) with dnaA, but for FASTA input and for long-read first assembled chromosomes. I have extended it to work with plasmids and phages, or for any input FASTA desired with `plassembler custom` or `plassembler mystery`.
+
+For bacterial chromosomes, `dnaapler chromosome` should ensure the chromosome breakpoint never interrupts genes or mobile genetic elements like prophages. It is intended to be used with good-quality completed bacterial genomes, generated with methods such as [Trycycler](https://github.com/rrwick/Trycycler/wiki), [Dragonflye](https://github.com/rpetit3/dragonflye) or my own pipleine [hybracter](https://github.com/gbouras13/hybracter).
+
+## Installation
+
+dnaapler requires only BLAST as an external dependency. 
+
+Installation from conda is recommended as this will install BLAST automatically when it becomes available.
+
+### Conda
+
+```
+conda install -c bioconda dnaapler
+```
+
+### Pip
+
+```
+pip install dnaapler
+```
+
+You will need to install BLAST separately.
+
+e.g.
+`conda install -c bioconda blast`
+
+
+
+Usage
+----------
+
+```
+Usage: dnaapler [OPTIONS] COMMAND [ARGS]...
+
+Options:
+  -h, --help     Show this message and exit.
+  -V, --version  Show the version and exit.
+
+Commands:
+  chromosome  Reorients your sequence to begin with the dnaA chromosomal...
+  citation    Print the citation(s) for this tool
+  custom      Reorients your sequence with a custom database
+  mystery     Reorients your sequence with a random gene
+  phage       Reorients your sequence to begin with the terL large...
+  plasmid     Reorients your sequence to begin with the repA replication...
+  ```
+
+  ```
+  Usage: dnaapler chromosome [OPTIONS]
+
+  Reorients your sequence to begin with the dnaA chromosomal replication
+  initiation gene
+
+Options:
+  -h, --help             Show this message and exit.
+  -V, --version          Show the version and exit.
+  -i, --input PATH       Path to input file in FASTA format  [required]
+  -o, --output PATH      Output directory   [default: output.dnaapler]
+  -t, --threads INTEGER  Number of threads to use with BLAST.  [default: 1]
+  -p, --prefix TEXT      Prefix for output files.  [default :dnaapler]
+  -f, --force            Force overwrites the output directory
+  ```
+
+
+
+Databases
+=============
+
+`dnaapler chromosome` uses 733 proteins downloaded from Swissprot with the query "Chromosomal replication initiator protein DnaA" on 24 May 2023 as its database for dnaA.
+
+`dnaapler plasmid` uses the repA database curated by Ryan Wick in [Unicycler](https://github.com/rrwick/Unicycler/blob/main/unicycler/gene_data/repA.fasta).
+
+`dnaapler phage` uses a terL database curated using [PHROGs](https://phrogs.lmge.uca.fr). I downloaded all the AA sequences of the 55 phrogs annotated as 'large terminase subunit', combined them depduplicated them using [seqkit](https://github.com/shenwei356/seqkit) `seqkit rmdup -s -o terL.faa phrog_terL.faa`.
+
+`dnaapler custom` uses a custom amino acid FASTA format gene(s) that you specify using `-c`. 
+
+The matching is strict - it requires a strong BLAST match (e-value 1E-10), and the first amino acid of a BLAST hit gene to be identified as Methionine, Valine or Leucine, the 3 most used start codons in bacteria/phages. 
+
+For the most commonly studied microbes (ESKAPE pathogens, etc), the dnaA database should suffice.
+
+If you try dnaapler on a more novel or under-studied microbe with a dnaA gene that has little sequence similarity to the database, you may need to provide your own dnaA gene(s) in amino acid FASTA format using `dnaapler custom`.
+
+After this [issue](https://github.com/gbouras13/dnaapler/issues/1), `dnaapler mystery` was added. It predicted all ORFs in the input, then picks a random sequence to re-orient your sequence with.s
+
+
+Motivation
+------------
+
+1. I couldn't get [Circlator](https://sanger-pathogens.github.io/circlator/) to work and it is no longer supported.
+2. [berokka](https://github.com/tseemann/berokka) doesn't orient chromosomes to begin with dnaa.
+3. After reading Ryan Wick's masterful bacterial genome assembly [tutorial](https://github.com/rrwick/Perfect-bacterial-genome-tutorial/wiki), I realised that it is probably optimal to run 2 polishing steps, once before then once after rotating the chromosome, to ensure the breakpoint is polished. Further, for some "complete" assemblies that didn't circularise properly, I figured that as long as you have a complete assembly (even if not "circular" as marked as in Flye), polishing after a re-orientation would be likely to circularise the chromosome. A bit like Ryan's [rotate_circular_gfa.py](https://github.com/rrwick/Perfect-bacterial-genome-tutorial/blob/main/scripts/rotate_circular_gfa.py) script, without the requirement of strict circularity.
+4. While researching MGEs in _S. aureus_ whole genome sequences, I repeatedly found instances where MGEs were interrupted by the chromosome breakpoint. So I thought I'd add a tool to automate it in my pipeline. 
+5. It's probably good to have all your sequences start at the same location for synteny analyses.
+
+Polishing Afterwards
+-----------
+
+I recommend that you undertake 2 rounds of polishing. The first prior to running dnaapler, and then again after. I'd highly recommend a conservative polisher like [Polypolish](https://github.com/rrwick/Polypolish) if you have short reads, otherwise 2 rounds of medaka.
+
+Acknowledgements
+=============
+
+Thanks to Torsten Seemann, Ryan Wick and the Circlator team for their existing work in the space. Also to [Michael Hall](https://github.com/mbhall88), whose repository [tbpore](https://github.com/mbhall88/tbpore) I took and adapted a lot of scaffolding code from because he writes really nice code, [Rob Edwards](https://github.com/linsalrob), because everything always comes back to phages, and especially [Vijini Mallawaarachchi](https://github.com/Vini2) who taught me how to actually do something resembling legitimate software development.
+
+
+

dnaapler-0.1.0/README.md

@@ -0,0 +1,118 @@
+[![CI](https://github.com/gbouras13/dnaapler/actions/workflows/ci.yaml/badge.svg)](https://github.com/gbouras13/dnaapler/actions/workflows/ci.yaml)
+[![codecov](https://codecov.io/gh/gbouras13/dnaapler/branch/refactor/graph/badge.svg?token=4B1T2PGM9V)](https://codecov.io/gh/gbouras13/dnaapler)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+
+# dnaapler
+
+Description
+----------
+
+`dnaapler` is a simple python program that takes a single nucleotide input sequence (in FASTA format), finds the desired start gene using `blastx` against an amino acid database, checks that the start of a gene is found, and if so, then reorients the chromosome to begin with this genes on the forward strand. 
+
+It was designed to replicate the reorientation functionality of [Unicycler](https://github.com/rrwick/Unicycler/blob/main/unicycler/gene_data/repA.fasta) with dnaA, but for FASTA input and for long-read first assembled chromosomes. I have extended it to work with plasmids and phages, or for any input FASTA desired with `plassembler custom` or `plassembler mystery`.
+
+For bacterial chromosomes, `dnaapler chromosome` should ensure the chromosome breakpoint never interrupts genes or mobile genetic elements like prophages. It is intended to be used with good-quality completed bacterial genomes, generated with methods such as [Trycycler](https://github.com/rrwick/Trycycler/wiki), [Dragonflye](https://github.com/rpetit3/dragonflye) or my own pipleine [hybracter](https://github.com/gbouras13/hybracter).
+
+## Installation
+
+dnaapler requires only BLAST as an external dependency. 
+
+Installation from conda is recommended as this will install BLAST automatically when it becomes available.
+
+### Conda
+
+```
+conda install -c bioconda dnaapler
+```
+
+### Pip
+
+```
+pip install dnaapler
+```
+
+You will need to install BLAST separately.
+
+e.g.
+`conda install -c bioconda blast`
+
+
+
+Usage
+----------
+
+```
+Usage: dnaapler [OPTIONS] COMMAND [ARGS]...
+
+Options:
+  -h, --help     Show this message and exit.
+  -V, --version  Show the version and exit.
+
+Commands:
+  chromosome  Reorients your sequence to begin with the dnaA chromosomal...
+  citation    Print the citation(s) for this tool
+  custom      Reorients your sequence with a custom database
+  mystery     Reorients your sequence with a random gene
+  phage       Reorients your sequence to begin with the terL large...
+  plasmid     Reorients your sequence to begin with the repA replication...
+  ```
+
+  ```
+  Usage: dnaapler chromosome [OPTIONS]
+
+  Reorients your sequence to begin with the dnaA chromosomal replication
+  initiation gene
+
+Options:
+  -h, --help             Show this message and exit.
+  -V, --version          Show the version and exit.
+  -i, --input PATH       Path to input file in FASTA format  [required]
+  -o, --output PATH      Output directory   [default: output.dnaapler]
+  -t, --threads INTEGER  Number of threads to use with BLAST.  [default: 1]
+  -p, --prefix TEXT      Prefix for output files.  [default :dnaapler]
+  -f, --force            Force overwrites the output directory
+  ```
+
+
+
+Databases
+=============
+
+`dnaapler chromosome` uses 733 proteins downloaded from Swissprot with the query "Chromosomal replication initiator protein DnaA" on 24 May 2023 as its database for dnaA.
+
+`dnaapler plasmid` uses the repA database curated by Ryan Wick in [Unicycler](https://github.com/rrwick/Unicycler/blob/main/unicycler/gene_data/repA.fasta).
+
+`dnaapler phage` uses a terL database curated using [PHROGs](https://phrogs.lmge.uca.fr). I downloaded all the AA sequences of the 55 phrogs annotated as 'large terminase subunit', combined them depduplicated them using [seqkit](https://github.com/shenwei356/seqkit) `seqkit rmdup -s -o terL.faa phrog_terL.faa`.
+
+`dnaapler custom` uses a custom amino acid FASTA format gene(s) that you specify using `-c`. 
+
+The matching is strict - it requires a strong BLAST match (e-value 1E-10), and the first amino acid of a BLAST hit gene to be identified as Methionine, Valine or Leucine, the 3 most used start codons in bacteria/phages. 
+
+For the most commonly studied microbes (ESKAPE pathogens, etc), the dnaA database should suffice.
+
+If you try dnaapler on a more novel or under-studied microbe with a dnaA gene that has little sequence similarity to the database, you may need to provide your own dnaA gene(s) in amino acid FASTA format using `dnaapler custom`.
+
+After this [issue](https://github.com/gbouras13/dnaapler/issues/1), `dnaapler mystery` was added. It predicted all ORFs in the input, then picks a random sequence to re-orient your sequence with.s
+
+
+Motivation
+------------
+
+1. I couldn't get [Circlator](https://sanger-pathogens.github.io/circlator/) to work and it is no longer supported.
+2. [berokka](https://github.com/tseemann/berokka) doesn't orient chromosomes to begin with dnaa.
+3. After reading Ryan Wick's masterful bacterial genome assembly [tutorial](https://github.com/rrwick/Perfect-bacterial-genome-tutorial/wiki), I realised that it is probably optimal to run 2 polishing steps, once before then once after rotating the chromosome, to ensure the breakpoint is polished. Further, for some "complete" assemblies that didn't circularise properly, I figured that as long as you have a complete assembly (even if not "circular" as marked as in Flye), polishing after a re-orientation would be likely to circularise the chromosome. A bit like Ryan's [rotate_circular_gfa.py](https://github.com/rrwick/Perfect-bacterial-genome-tutorial/blob/main/scripts/rotate_circular_gfa.py) script, without the requirement of strict circularity.
+4. While researching MGEs in _S. aureus_ whole genome sequences, I repeatedly found instances where MGEs were interrupted by the chromosome breakpoint. So I thought I'd add a tool to automate it in my pipeline. 
+5. It's probably good to have all your sequences start at the same location for synteny analyses.
+
+Polishing Afterwards
+-----------
+
+I recommend that you undertake 2 rounds of polishing. The first prior to running dnaapler, and then again after. I'd highly recommend a conservative polisher like [Polypolish](https://github.com/rrwick/Polypolish) if you have short reads, otherwise 2 rounds of medaka.
+
+Acknowledgements
+=============
+
+Thanks to Torsten Seemann, Ryan Wick and the Circlator team for their existing work in the space. Also to [Michael Hall](https://github.com/mbhall88), whose repository [tbpore](https://github.com/mbhall88/tbpore) I took and adapted a lot of scaffolding code from because he writes really nice code, [Rob Edwards](https://github.com/linsalrob), because everything always comes back to phages, and especially [Vijini Mallawaarachchi](https://github.com/Vini2) who taught me how to actually do something resembling legitimate software development.
+
+

dnaapler-0.1.0/pyproject.toml

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+[tool.poetry]
+name = "dnaapler"
+version = "0.1.0" # change VERSION too
+description = "Reorients assembled microbial sequences"
+authors = ["George Bouras <george.bouras@adelaide.edu.au>"]
+license = "MIT"
+readme = "README.md"
+homepage = "https://github.com/gbouras13/dnaapler"
+repository = "https://github.com/gbouras13/dnaapler"
+keywords = ["microbial", "bioinformatics"]
+include = [
+    "HISTORY.md"
+]
+
+[tool.poetry.scripts]
+dnaapler = 'dnaapler:main'
+
+[tool.poetry.dependencies]
+python = ">=3.8,<4.0"
+click = ">=8.0.0"
+loguru = ">=0.5.3"
+pyyaml = ">=6.0"
+pandas = ">=1.4.2"
+biopython = ">=1.76"
+pyrodigal = ">=2.0.0"
+
+
+[tool.poetry.dev-dependencies]
+black = ">=22.3.0"
+isort = ">=5.10.1"
+pytest = ">=6.2.5"
+pytest-cov = ">=3.0.0"
+flake8 = ">=3.0.1"
+
+[[tool.poetry.source]]
+name = "pypi-test"
+url = "https://test.pypi.org/simple/"
+priority = "primary"
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.isort]
+profile = "black"