Scripts used for handling and analysing my E. coli genome assembly collection.
The workflow starts by pulling genome assemblies from ENA using a saved search result from the site.
- Enter a search term into ENA search
- Select Assembly results
- Download ENA records: XML
- Create an output directory
- Run fasta_from_ena.py with XML file as input and directory created as output
- A summary Excel file is created from search result
- Wait for FASTA files to be downloaded and unzipped. This can take a while...
- Run fetch_Entrez_metadata.py with directory as positional argument (you can include Entrez API and your account email to speed up the run)
For serotyping:
- Use the Ectyper tool on Galaxy
- Download results into a folder
- Run utils.py with
-s
or--sero
flag to input path for directory containing serotpe data.--input
should be path for working directory
For phylotyping:
- Run utils.py with
--input
flag for working directory and use-p
or--phylo
flag. - Optionally, you can specify location of EzClermont.py script using
--script
, but script is included in package.
- Run
setup_conda
script in command-line or - Run:
$ conda env create --name ecoli-collection --file environment.yaml
$ conda activate ecoli-collection
- Have XML file in EcoliCollection directory
- Rename XML file to
ena_genome_assembly.xml
- Run
snakemake --cores 1
This is working progress:
- Tidy scripts
- Add docstrings
- Make changes to EzClermont
- Finish README
- Include tutorial
- Trialed and tested
- CLI support
- Snakemake support
- conda support
- Have Excel spreadsheet by put in parent directory instead of FASTA directory