Genomebaser is a tool to manage complete genomes from the NCBI
Check if 3rd party dependencies (non-python) exist
Use rsync to manage periodic updates
Examples:
>>> fetch_genomes("Escherichia coli")
>>>
>>> fetch_genomes("Klebsiella pneumoniae", "/home/me/dbs/")
Parameters: | target_genus_species – the genus species as a string (space delimited) |
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Returns: | the database location |
Converts GenBank to fasta while naming using the given in the DEFINITION
Examples:
>>> genbank_to_fasta("/home/mscook/dbs/Klebsiella_pneumoniae"
Parameters: | db_loc – the fullpath as a sting to the database location (genus species inclusive) |
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Returns: | a list of the output fasta files |
Make a prokka database of the complete genomes
Parameters: |
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Separate complete genomes from plasmids
Parameters: |
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Returns: | a list of DEFINITION format named GenBank files |