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python-biopython  1.60
Namespaces | Functions
Bio.ExPASy Namespace Reference

Namespaces

namespace  Enzyme
namespace  Prodoc
namespace  Prosite
namespace  ScanProsite

Functions

def get_prodoc_entry
def get_prosite_entry
def get_prosite_raw
def get_sprot_raw
def sprot_search_ful
def sprot_search_de

Function Documentation

def Bio.ExPASy.get_prodoc_entry (   id,
  cgi = 'http://www.expasy.ch/cgi-bin/get-prodoc-entry' 
)
get_prodoc_entry(id,
cgi='http://www.expasy.ch/cgi-bin/get-prodoc-entry') -> handle

Get a handle to a PRODOC entry at ExPASy in HTML format. 

For a non-existing key XXX, ExPASy returns an HTML-formatted page
containing this line:
'There is no PROSITE documentation entry XXX. Please try again.'

Definition at line 23 of file __init__.py.

00023 
00024 def get_prodoc_entry(id, cgi='http://www.expasy.ch/cgi-bin/get-prodoc-entry'):
00025     """get_prodoc_entry(id,
00026     cgi='http://www.expasy.ch/cgi-bin/get-prodoc-entry') -> handle
00027 
00028     Get a handle to a PRODOC entry at ExPASy in HTML format. 
00029 
00030     For a non-existing key XXX, ExPASy returns an HTML-formatted page
00031     containing this line:
00032     'There is no PROSITE documentation entry XXX. Please try again.'
00033     """
00034     # Open a handle to ExPASy.
00035     handle = urllib.urlopen("%s?%s" % (cgi, id))
00036     return handle

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def Bio.ExPASy.get_prosite_entry (   id,
  cgi = 'http://www.expasy.ch/cgi-bin/get-prosite-entry' 
)
get_prosite_entry(id,
cgi='http://www.expasy.ch/cgi-bin/get-prosite-entry') -> handle

Get a handle to a PROSITE entry at ExPASy in HTML format.

For a non-existing key XXX, ExPASy returns an HTML-formatted page
containing this line:
'There is currently no PROSITE entry for XXX. Please try again.'

Definition at line 38 of file __init__.py.

00038 
00039                       cgi='http://www.expasy.ch/cgi-bin/get-prosite-entry'):
00040     """get_prosite_entry(id,
00041     cgi='http://www.expasy.ch/cgi-bin/get-prosite-entry') -> handle
00042 
00043     Get a handle to a PROSITE entry at ExPASy in HTML format.
00044 
00045     For a non-existing key XXX, ExPASy returns an HTML-formatted page
00046     containing this line:
00047     'There is currently no PROSITE entry for XXX. Please try again.'
00048     """
00049     handle = urllib.urlopen("%s?%s" % (cgi, id))
00050     return handle

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def Bio.ExPASy.get_prosite_raw (   id,
  cgi = 'http://www.expasy.ch/cgi-bin/get-prosite-raw.pl' 
)
get_prosite_raw(id,
                   cgi='http://www.expasy.ch/cgi-bin/get-prosite-raw.pl')
-> handle

Get a handle to a raw PROSITE or PRODOC entry at ExPASy.

For a non-existing key, ExPASy returns nothing.

Definition at line 51 of file __init__.py.

00051 
00052 def get_prosite_raw(id, cgi='http://www.expasy.ch/cgi-bin/get-prosite-raw.pl'):
00053     """get_prosite_raw(id,
00054                        cgi='http://www.expasy.ch/cgi-bin/get-prosite-raw.pl')
00055     -> handle
00056 
00057     Get a handle to a raw PROSITE or PRODOC entry at ExPASy.
00058 
00059     For a non-existing key, ExPASy returns nothing.
00060     """
00061     handle = urllib.urlopen("%s?%s" % (cgi, id))
00062     return handle

Get a handle to a raw SwissProt entry at ExPASy.

For an ID of XXX, fetches http://www.uniprot.org/uniprot/XXX.txt
(as per the http://www.expasy.ch/expasy_urls.html documentation).

Definition at line 63 of file __init__.py.

00063 
00064 def get_sprot_raw(id):
00065     """Get a handle to a raw SwissProt entry at ExPASy.
00066 
00067     For an ID of XXX, fetches http://www.uniprot.org/uniprot/XXX.txt
00068     (as per the http://www.expasy.ch/expasy_urls.html documentation).
00069     """
00070     return urllib.urlopen("http://www.uniprot.org/uniprot/%s.txt" % id)

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def Bio.ExPASy.sprot_search_de (   text,
  swissprot = 1,
  trembl = None,
  cgi = 'http://www.expasy.ch/cgi-bin/sprot-search-de' 
)
sprot_search_de(text, swissprot=1, trembl=None,
cgi='http://www.expasy.ch/cgi-bin/sprot-search-de') -> handle

Search SwissProt by name, description, gene name, species, or
organelle.

Definition at line 92 of file __init__.py.

00092 
00093                     cgi='http://www.expasy.ch/cgi-bin/sprot-search-de'):
00094     """sprot_search_de(text, swissprot=1, trembl=None,
00095     cgi='http://www.expasy.ch/cgi-bin/sprot-search-de') -> handle
00096 
00097     Search SwissProt by name, description, gene name, species, or
00098     organelle.
00099 
00100     """
00101     variables = {'SEARCH' : text}
00102     if swissprot:
00103         variables['S'] = 'on'
00104     if trembl:
00105         variables['T'] = 'on'
00106     options = urllib.urlencode(variables)
00107     fullcgi = "%s?%s" % (cgi, options)
00108     handle = urllib.urlopen(fullcgi)
00109     return handle

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def Bio.ExPASy.sprot_search_ful (   text,
  make_wild = None,
  swissprot = 1,
  trembl = None,
  cgi = 'http://www.expasy.ch/cgi-bin/sprot-search-ful' 
)
sprot_search_ful(text, make_wild=None, swissprot=1, trembl=None,
cgi='http://www.expasy.ch/cgi-bin/sprot-search-ful') -> handle

Search SwissProt by full text.

Definition at line 72 of file __init__.py.

00072 
00073                      cgi='http://www.expasy.ch/cgi-bin/sprot-search-ful'):
00074     """sprot_search_ful(text, make_wild=None, swissprot=1, trembl=None,
00075     cgi='http://www.expasy.ch/cgi-bin/sprot-search-ful') -> handle
00076 
00077     Search SwissProt by full text.
00078 
00079     """
00080     variables = {'SEARCH' : text}
00081     if make_wild:
00082         variables['makeWild'] = 'on'
00083     if swissprot:
00084         variables['S'] = 'on'
00085     if trembl:
00086         variables['T'] = 'on'
00087     options = urllib.urlencode(variables)
00088     fullcgi = "%s?%s" % (cgi, options)
00089     handle = urllib.urlopen(fullcgi)
00090     return handle

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