eutils is a Python package dedicated to searching for, fetching, and parsing records from NCBI using their E-utilities interface.
STATUS: This code is alpha. There are no known bugs, but the code supports only a limited subset of E-Utilities replies
- optional sqlite-based caching of compressed replies
- automatic throttling
- simple Pythonic interface for searching and fetching
- "façades" over XML from replies provide access to essential attributes
In [1]: import eutils.client
In [2]: esr = ec.esearch(db='gene',term='tumor necrosis factor')
In [3]: gb = ec.efetch(db='gene',id=esr.ids[0])
In [4]: gb.locus, gb.maploc, gb.description, gb.type
Out[4]: ('TP53', '17p13.1', 'tumor protein p53', 'protein-coding')
In [5]: [ str(r) for r in gb.references ]
Out[5]:
['GeneCommentary(acv=NC_000017.10,type=genomic,heading=Reference GRCh37.p13 Primary Assembly,label=chromosome 17 reference GRCh37.p13 Primary Assembly)',
'GeneCommentary(acv=NG_017013.2,type=genomic,heading=Reference assembly,label=RefSeqGene)',
'GeneCommentary(acv=NC_018928.2,type=genomic,heading=Alternate CHM1_1.1,label=chromosome 17 alternate CHM1_1.1)',
'GeneCommentary(acv=AC_000149.1,type=genomic,heading=Alternate HuRef,label=chromosome 17 alternate HuRef)']
In [6]: gb.references[0].acv
Out[6]: 'NC_000017.10'
In [7]: gb.references[0].products[0].acv
Out[7]: 'NM_001126112.2'
In [8]: gb.references[0].products[0].genomic_coords.strand
Out[8]: -1
In [9]: gb.references[0].products[0].genomic_coords.intervals
Out[9]:
[(7590694, 7590868),
(7579838, 7579937),
(7579699, 7579721),
(7579311, 7579590),
(7578370, 7578554),
(7578176, 7578289),
(7577498, 7577608),
(7577018, 7577155),
(7576852, 7576926),
(7573926, 7574033),
(7571719, 7573008)]