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I need to download all the completely assembled cyanobacterial genome's GenBank file(.gbff) from NCBI(RefSeq or INSDC ftp data).

For this I think, the steps are:

  1. Need to find the completely assembled genomes.
  2. find the GenBank file URL based on the taxonomic name.
  3. download the GenBank file(.gbff file)

Is their any way to do this by using any python module or any other idea??

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  • $\begingroup$ Biopython has tools that could help you for steps 2 and 3, but I'm not sure how to get the information of your step 1. $\endgroup$
    – bli
    Sep 5 '18 at 7:23
  • $\begingroup$ can you please tell the tool name for step 2. $\endgroup$ Sep 5 '18 at 7:25
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    $\begingroup$ @Arijit Searching for "Download biopython Genebank" lead you here $\endgroup$
    – llrs
    Sep 5 '18 at 7:31
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Outline of solution:

Edit:
Since I will need something like that soon, I made a Perl script for downloading genomes.
For Cyanobacteria, you would do ./download-refseq-genomes.pl 1117

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As an alternative, you can use the NCBI Datasets CLI, in a two step process to generate a dehydrated dataset for later hydration:

# Download metadata for all Cyanobacteria 
# And pull out accession for 'Complete' genomes
./datasets assembly-descriptors taxon Cyanobacteria --limit ALL \
     | jq -r '.assemblies[].assembly | "\(.assembly_accession) \(.assembly_level)"' \
     | grep Complete \
     | cut -f 1 -d ' ' > accs.txt

# Download a dehydrated dataset for the provided set of accessions
./datasets download assembly -i accs.txt -f 1117_complete.zip \
     --dehydrated \
     --exclude-protein \
     --exclude-rna \
     --exclude-seq \
     --exclude-gff3 \
     --include-gbff 

You may be interested in some of the other files that are excluded.

Once you have the dehydrated dataset, you can rehydrate it when you are ready to analyze the data with:

unzip 1117_complete.zip -d 1117_complete
./datasets rehydrate -f 1117_complete
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