Package Bio :: Package EUtils :: Module parse
[hide private]
[frames] | no frames]

Module parse

source code

Classes [hide private]
  GetObject
  UsePOMParser
Functions [hide private]
 
_construct_pattern() source code
 
_load_module(name) source code
 
_check_for_errors(pom) source code
 
_check_for_bad_input_stream(infile, force_encoding=1) source code
 
parse_search(infile, webenv_ref=[None]) source code
 
parse_post(infile, webenv_ref) source code
 
convert_summary_Date(x) source code
 
convert_summary_Date_string(s) source code
 
unescape_entities(s) source code
 
convert_summary_String(x) source code
 
convert_summary_Integer(x) source code
 
convert_summary_Unknown(x) source code
 
convert_summary_List(x) source code
 
convert_summary_Items(x) source code
 
parse_summary_xml(infile) source code
 
parse_fetch_publication_xml(infile) source code
 
parse_fetch_sequence_xml(infile) source code
 
parse_fetch_identifiers(infile) source code
 
_check_for_link_errors(pom) source code
 
_parse_link(infile) source code
 
parse_neighbor_links(infile) source code
 
parse_lcheck(infile) source code
 
parse_ncheck(infile) source code
 
_get_opt_string(ele, name) source code
 
parse_llinks(infile) source code
 
parse_prlinks(infile) source code
 
parse_link_xml(infile) source code
Variables [hide private]
  _pubdate_format1 = re.compile(r'(?P<year>\d{4})( (?P<month>[A-...
  _pubdate_format2 = re.compile(r'(?P<year>\d{4}) (?P<month1>[A-...
  _month_names_to_number = {None: 1, 'Apr': 4, 'Aug': 8, 'Dec': ...
  _entrezdate_format = re.compile(r'(?P<year>\d+)/(?P<month>\d+)...
  summary_type_parser_table = {"String": convert_summary_String,...
  __package__ = 'Bio.EUtils'
  _entity_pattern = re.compile(r'&([a-zA-Z]{1,8});')
  entitydefs = {'AElig': u'Æ', 'Aacute': u'Á', 'Acirc': u'Â', 'A...
Variables Details [hide private]

_pubdate_format1

Value:
re.compile(r'(?P<year>\d{4})( (?P<month>[A-Za-z]{3})( (?P<day>\d+))?)?\
$')

_pubdate_format2

Value:
re.compile(r'(?P<year>\d{4}) (?P<month1>[A-Za-z]{3})-(?P<month2>[A-Za-\
z]{3})')

_month_names_to_number

Value:
{None: 1,
 'Apr': 4,
 'Aug': 8,
 'Dec': 12,
 'Feb': 2,
 'Jan': 1,
 'Jul': 7,
 'Jun': 6,
...

_entrezdate_format

Value:
re.compile(r'(?P<year>\d+)/(?P<month>\d+)/(?P<day>\d+)')

summary_type_parser_table

Value:
{"String": convert_summary_String, "Integer": convert_summary_Integer,\
 "Unknown": convert_summary_Unknown, "Date": convert_summary_Date, "Li\
st": convert_summary_List,}

entitydefs

Value:
{'AElig': u'Æ',
 'Aacute': u'Á',
 'Acirc': u'Â',
 'Agrave': u'À',
 'Alpha': u'Α',
 'Aring': u'Å',
 'Atilde': u'Ã',
 'Auml': u'Ä',
...