Package Bio :: Package EUtils :: Module DBIdsClient
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Module Bio.EUtils.DBIdsClient

Search and retrieve information given a set of database identifiers.

EUtils has two major modes. One uses history while the other uses database identifiers. This is a high-level interface for working with identifiers. You should use this module to get information about a set of known database identifiers.

See HistoryClient if you want to work with a large number of identifiers or potentially large search results.
>>> from Bio import EUtils
>>> from Bio.EUtils import DBIdsClient
>>> client = DBIdsClient.DBIdsClient()
>>> result = client.search("dalke", retmax = 100)
>>> len(result)
30

>>> print result[0].efetch(retmode = "text", rettype = "abstract").read()

1: Pac Symp Biocomput 1997;:85-96

Using Tcl for molecular visualization and analysis.

Dalke A, Schulten K.

Beckman Institute, Urbana, IL 61801, USA.

Reading and manipulating molecular structure data is a standard task in every molecular visualization and analysis program, but is rarely available in a form readily accessible to the user. Instead, the development of new methods for analysis, display, and interaction is often achieved by writing a new program, rather than building on pre-existing software. We present the Tcl-based script language used in our molecular modeling program, VMD, and show how it can access information about the molecular structure, perform analysis, and graphically display and animate the results. The commands are available to the user and make VMD a useful environment for studying biomolecules.

PMID: 9390282 [PubMed - indexed for MEDLINE]

>>>

Find sequences similar to GI:4579714 which were published in 2002.
>>> protein = DBIdsClient.from_dbids(EUtils.DBIds("protein", "4579714"))
>>> neighbors = protein.neighbor_links("protein",
...        daterange = EUtils.DateRange("2002/01/01", "2002/12/31", "pdat"))
>>> dbids = neighbors.linksetdbs["protein_protein"].dbids
>>> len(dbids)
28

>>> print dbids
DBIds(u'protein', [u'4579714', u'25298947', u'24158913', u'24158914', u'24158915', u'17942993', u'17942994', u'17942995', u'20150921', u'20150922', u'20151159', u'25298949', u'19716034', u'20663737', u'20663738', u'20663741', u'24987328', u'25533128', u'25298946', u'25298948', u'23008597', u'20219020', u'21218340', u'21218344', u'19075395', u'21218338', u'21218342', u'21311795'])

>>> 
>>> print client.from_dbids(dbids[:5]).efetch(retmode="text",
...                                           rettype="summary").read()

1: BAA75200 Bacteriorhodopsin [Halobacterium sp.] gi|4579714|dbj|BAA75200.1|[4579714]

2: H84300 bacteriorhodopsin [imported] - Halobacterium sp. NRC-1 gi|25298947|pir||H84300[25298947]

3: 1M0KA Chain A, Bacteriorhodopsin K Intermediate At 1.43 A Resolution gi|24158913|pdb|1M0K|A[24158913]

4: 1M0LA Chain A, BacteriorhodopsinLIPID COMPLEX AT 1.47 A RESOLUTION gi|24158914|pdb|1M0L|A[24158914]

5: 1M0MA Chain A, Bacteriorhodopsin M1 Intermediate At 1.43 A Resolution gi|24158915|pdb|1M0M|A[24158915]

>>>
Classes
BaseDBIdsRecordSet Base class for dealing with a set of records, reference by identifier
DBIdsClient Create a RecordSet either from a search or a set of dbids
DBIdsLookup Look up information about a DBIds
DBIdsRecord A single record on the server
PublicationDBIdsFetchMixin Support 'efetch' for publication records
PublicationDBIdsRecord a single publication record, referenced by database identifier
PublicationDBIdsRecordSet a set of publication records, referenced by database identifier
SequenceDBIdsFetchMixin Support 'efetch' for sequence records
SequenceDBIdsRecord a single sequence record, referenced by database identifier
SequenceDBIdsRecordSet a set of sequence records, referenced by database identifier

Function Summary
  from_dbids(dbids, dbtype, eutils)
create a RecordSet interface for the set of database identifiers Parameters are: dbids -- a DBIds dbtype -- the dbtype to use (EUtils.Config.{SEQUENCE,PUBLIATION}_TYPE) in case dbids.db isn't in the list of know NCBI databases.
  _get_recordset_constructor(db, dbtype)
get the right DataSet constructor for a database

Function Details

from_dbids(dbids, dbtype=None, eutils=None)

create a RecordSet interface for the set of database identifiers

Parameters are:
  dbids -- a DBIds
  dbtype -- the dbtype to use (EUtils.Config.{SEQUENCE,PUBLIATION}_TYPE)
       in case dbids.db isn't in the list of know NCBI databases.
       Defaults to None.
  eutils -- the ThinClient to use, defaults to creating a new
       ThinClient.ThinClient()

_get_recordset_constructor(db, dbtype)

get the right DataSet constructor for a database

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