Combine acc2gb.py and fetchseq.py, putting db and rettype as arguments

The scripts acc2gb.py and fetchseq.py do essentially the same thing: they use the Entrez system to download data from NCBI.

We can combine them into a single, multi-purpose script by removing some of the hard-coded parameters and making them command line arguments. We’ll keep the acc2gb.py script and delete fetchseq.py since it has fewer calls and @aays knows what they are.

These are the changes that need to be made:

• Remove hardcoded db parameter on line 22 and make it a command line argument
• Remove hardcoded rettype parameter on line 33 and make it a command line argument
• Add parameter retmode="text" on line 33, same as in fetchseq.py.
• Include in the documentation what ‘db’ and ‘rettype’ mean and which arguments would be used in which situations. For now, these are the two we’ve been using:
• Case 1: rettype = gbwithparts, db = nuccore - downloads genbank file with metadata and fasta DNA sequence (i.e. for downloading bacterial genomes with metadata)
• Case 2: rettype = fasta, db = protein - downloads fasta file with protein sequence (i.e. for downloading antiCRISPR protein sequences for BLAST)
• Delete fetchseq.py.

Submit a PR to the master branch when complete! If you have any questions at all, ping me or @aays and we’ll get back to you ASAP.

[morrme]

@mbonsma @aays ready for review 😃

[mbonsma]

@morrme true, good point. We can leave that one out then.