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NCBI.py
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
The main Blast web page is available at:
http://www.ncbi.nlm.nih.gov/BLAST/
Functions:
query Query Entrez.
pmfetch Retrieve results using a unique identifier.
pmqty Search PubMed.
pmneighbor Return a list of related articles for a PubMed entry.
_open
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Imported modules
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from Bio import File
import string
import urllib
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Functions
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_open
pmfetch
pmneighbor
pmqty
query
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_open
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_open (
cgi,
params={},
get=1,
)
_open(cgi, params={}, get=1) -> UndoHandle
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. get is a boolean
that describes whether a GET should be used. Does some
simple error checking, and will raise an IOError if it encounters one.
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Exceptions
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IOError, "500 Proxy Error (NCBI busy?)"
IOError, "502 Proxy Error (NCBI busy?)"
IOError, "ERROR, possibly because id not available?"
IOError, "WWW Error 500 Diagnostic (NCBI busy?)"
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pmfetch
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pmfetch (
db,
id,
report=None,
mode=None,
cgi="http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi",
)
pmfetch(db, id, report=None, mode=None,
cgi="http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi") Query PmFetch and return a handle to the results. See the
online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch_help.html
Raises an IOError exception if there's a network error.
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pmneighbor
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pmneighbor (
pmid,
display,
cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgi',
)
pmneighbor(pmid, display,
cgi=http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgi) -> handle Query PMNeighbor and return a handle to the results. See the
online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor_help.html
Raises an IOError exception if there's a network error.
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pmqty
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pmqty (
db,
term,
dopt=None,
cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi',
**keywds,
)
pmqty(db, term, dopt=None,
cgi=http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi) -> handle Query PmQty and return a handle to the results. See the
online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty_help.html
Raises an IOError exception if there's a network error.
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query
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query (
cmd,
db,
cgi='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi',
**keywds,
)
query(cmd, db, cgi=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi,
**keywds) -> handle Query Entrez and return a handle to the results. See the online
documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/linking.html
Raises an IOError exception if there's a network error.
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