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Provides code to access NCBI over the WWW. The main Entrez web page is available at: http://www.ncbi.nlm.nih.gov/Entrez/ A list of the Entrez utilities is available at: http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html Functions: efetch Retrieves records in the requested format from a list of one or more primary IDs or from the user's environment epost Posts a file containing a list of primary IDs for future use in the user's environment to use with subsequent search strategies esearch Searches and retrieves primary IDs (for use in EFetch, ELink, and ESummary) and term translations and optionally retains results for future use in the user's environment. elink Checks for the existence of an external or Related Articles link from a list of one or more primary IDs. Retrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and Attributes for multiple IDs. einfo Provides field index term counts, last update, and available links for each database. esummary Retrieves document summaries from a list of primary IDs or from the user's environment. egquery Provides Entrez database counts in XML for a single search using Global Query. espell Retrieves spelling suggestions. read Parses the XML results returned by any of the above functions. Typical usage is: >>> handle = Entrez.einfo() # or esearch, efetch, ... >>> record = Entrez.read(handle) where record is now a Python dictionary or list. _open Internally used function.
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Query Entrez and return a handle to the HTML results (DEPRECATED). See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helplinks.chapter.linkshelp Return a handle to the results. Raises an IOError exception if there's a network error. |
Post a file of identifiers for future use. Posts a file containing a list of UIs for future use in the user's environment to use with subsequent search strategies. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/query/static/epost_help.html Return a handle to the results. Raises an IOError exception if there's a network error. |
Fetches Entrez results which are returned as a handle. EFetch retrieves records in the requested format from a list of one or more UIs or from user's environment. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html Return a handle to the results. Raises an IOError exception if there's a network error. Short example: from Bio import Entrez handle = Entrez.efetch(db="nucleotide", id="57240072", rettype="genbank") print handle.read() |
ESearch runs an Entrez search and returns a handle to the results. ESearch searches and retrieves primary IDs (for use in EFetch, ELink and ESummary) and term translations, and optionally retains results for future use in the user's environment. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html Return a handle to the results which are always in XML format. Raises an IOError exception if there's a network error. Short example: from Bio import Entez handle = Entrez.esearch(db="nucleotide", retmax=10, term="Opuntia") record = Entrez.read(handle) print record["Count"] print record["IdList"] |
ELink checks for linked external articles and returns a handle. ELink checks for the existence of an external or Related Articles link from a list of one or more primary IDs; retrieves IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and attributes for multiple IDs. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/query/static/elink_help.html Return a handle to the results, by default in XML format. Raises an IOError exception if there's a network error. |
EInfo returns a summary of the Entez databases as a results handle. EInfo provides field names, index term counts, last update, and available links for each Entrez database. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/query/static/einfo_help.html Return a handle to the results, by default in XML format. Raises an IOError exception if there's a network error. Short example: from Bio import Entrez record = Entrez.read(Entrez.einfo()) print record['DbList'] |
ESummary retrieves document summaries as a results handle. ESummary retrieves document summaries from a list of primary IDs or from the user's environment. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/query/static/esummary_help.html Return a handle to the results, by default in XML format. Raises an IOError exception if there's a network error. |
EGQuery provides Entrez database counts for a global search. EGQuery provides Entrez database counts in XML for a single search using Global Query. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/query/static/egquery_help.html Return a handle to the results in XML format. Raises an IOError exception if there's a network error. |
ESpell retrieves spelling suggestions, returned in a results handle. ESpell retrieves spelling suggestions, if available. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/query/static/espell_help.html Return a handle to the results, by default in XML format. Raises an IOError exception if there's a network error. Short example: from Bio import Entrez record = Entrez.read(Entrez.espell(term="biopythooon")) print record["Query"] print record["CorrectedQuery"] |
Parses an XML file from the NCBI Entrez Utilities into python objects. This function parses an XML file created by NCBI's Entrez Utilities, returning a multilevel data structure of Python lists and dictionaries. Most XML files returned by NCBI's Entrez Utilities can be parsed by this function, provided its DTD is available. Biopython includes the DTDs for most commonly used Entrez Utilities. Whereas the data structure seems to consist of generic Python lists, dictionaries, strings, and so on, each of these is actually a class derived from the base type. This allows us to store the attributes (if any) of each element in a dictionary my_element.attributes, and the tag name in my_element.tag. |
Helper function to build the URL and open a handle to it (PRIVATE). Open a handle to Entrez. cgi is the URL for the cgi script to access. params is a dictionary with the options to pass to it. Does some simple error checking, and will raise an IOError if it encounters one. This function also enforces the "three second rule" to avoid abusing the NCBI servers. |
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