tirganteanga/ecolicollection

Scripts used for handling my E coli assemblies collection

EcoliCollection

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.

Tutorial

1. Enter a search term into ENA search
2. Select Assembly results
3. Download ENA records: XML
4. Create an output directory
5. Run fasta_from_ena.py with XML file as input and directory created as output
6. A summary Excel file is created from search result
7. Wait for FASTA files to be downloaded and unzipped. This can take a while...
8. 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:

1. Use the Ectyper tool on Galaxy
2. Download results into a folder
3. 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:

1. Run utils.py with --input flag for working directory and use -p or --phylo flag.
2. Optionally, you can specify location of EzClermont.py script using --script, but script is included in package.

Conda support

1. Run setup_conda script in command-line or
2. Run:

$ conda env create --name ecoli-collection --file environment.yaml
$ conda activate ecoli-collection

Snakemake support

1. Have XML file in EcoliCollection directory
2. Rename XML file to ena_genome_assembly.xml
3. Run snakemake --cores 1

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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