Fetch NCBI data efficiently
Project description
NCBI DAtaREtrival
Retrives your NCBI search results and through Entrez in a user friendly way.
Installation
Run the following to install:
pip install ncbiget
Usage
# retrives results from NCBI and writes it to a csv file (Accession ID and Definition)
# query: search details count: number of items filename: output file name
from ncbiget import get_genbank
get_genbank(query="Klebsiella pneumoniae", count=1, filename="results.csv") # default
#to get list of unique strains from the csv file
#MAKE SURE THE FORMAT OF THE CSV FILE IS SIMILAR TO THE RESULT FILE FROM get_genbank() i.e. Descriptions should be in column 3
# filename: input file name
from ncbiget import get_strains
get_strains(filename="results.csv") # default
#to get fasta file of each strain
#MAKE SURE THE FORMAT OF THE CSV FILE IS SIMILAR TO THE RESULT FILE FROM get_genbank() i.e. Descriptions should be in column 3
# filename: input file name
from ncbiget import get_fasta
get_fasta(filename="results.csv") # default
Developing ncbidare
To install ncbidare along with the tools you need to develop and run tests, run the following in your virtualenv:
pip install -e .[dev]
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