Using DendroPy to Download GenBank Data

download_wobbegong_gb.py

#! /usr/bin/env python

from dendropy.interop import ncbi

entrez = ncbi.Entrez(generate_labels=True,
            label_num_desc_components=2,
            label_separator='_',
            exclude_gbnum_from_label=True,
            sort_taxa_by_label=True)

cr_ids = ["EU%d" % i for i in range(888892, 888900)] + \
        ["DQ885482", "DQ885485", "DQ885486"]
atpase_ids = ["EU%d" % i for i in range(910196, 910206)] + \
        ["DQ886665", "DQ886667", "DQ886668"]
s7_nums = range(379563, 379566) + range(910206, 910215)
s7_ids = ["EU%d" % i for i in s7_nums]

name_ids_map = { "cr" : cr_ids, "atpase" : atpase_ids, "s7" : s7_ids }
output_prefix = "wobbegong"
for name, ids in name_ids_map.items():
    data = entrez.fetch_nucleotide_accessions(ids)
    data.write_to_path(output_prefix + "_" + name + ".unaligned.fasta",
            "fasta")