Package Bio :: Module Std
[hide private]
[frames] | no frames]

Module Std

source code

This module is DEPRECATED.

Andrew Dalke is no longer maintaining Martel or Bio.Mindy, and these modules and associate ones like Bio.Std are now deprecated. They are no longer used in any of the current Biopython parsers, and are likely to be removed in a future release.

Classes [hide private]
  StdTerm
Functions [hide private]
 
_set_if_given(attrs, field, d, valid=None, convert=None) source code
 
_complain_if_given(attrs, name) source code
 
_must_have(expr, f) source code
 
_must_have_set(expr, sets) source code
 
_must_not_have(expr, f) source code
 
_check_name(f, text) source code
 
_check_attrs(attrs, names) source code
 
_settag(f, tag) source code
 
record(expr, attrs={}) source code
 
dbid(expr, attrs={}) source code
 
description_block(expr, attrs={}) source code
 
description(expr, attrs={}) source code
 
description_line(expr, attrs={}) source code
 
fast_dbxref(expr, attrs={}) source code
 
dbxref(expr, attrs={}) source code
 
dbxref_dbname(expr, attrs={}) source code
 
dbxref_dbid(expr, attrs={}) source code
 
dbxref_negate(expr, attrs={}) source code
 
_check_gapchar(s) source code
 
sequence_block(expr, attrs={}) source code
 
sequence(expr, attrs={}) source code
 
alphabet(expr, attrs={}) source code
 
feature_block(expr, attrs={}) source code
 
feature(expr, attrs={}) source code
 
feature_name(expr, attrs={}) source code
 
feature_location(expr, attrs={}) source code
 
feature_location_start(expr, attrs={}) source code
 
feature_location_end(expr, attrs={}) source code
 
feature_description(expr, attrs={}) source code
 
feature_qualifier(expr, attrs={}) source code
 
feature_qualifier_name(expr, attrs={}) source code
 
feature_qualifier_description(expr, attrs={}) source code
 
application_name(expr, attrs={}) source code
 
application_version(expr, attrs={}) source code
 
search_header(expr, attrs={}) source code
 
search_table(expr, attrs={}) source code
 
search_table_description(expr, attrs={}) source code
 
search_table_value(expr, attrs={}) source code
 
search_table_entry(expr, attrs={}) source code
 
query_description_block(expr, attrs={}) source code
 
query_description(expr, attrs={}) source code
 
query_size(expr, attrs={}) source code
 
database_name(expr, attrs={}) source code
 
database_num_sequences(expr, attrs={}) source code
 
database_num_letters(expr, attrs={}) source code
 
hit(expr, attrs={}) source code
 
hit_length(expr, attrs={}) source code
 
hit_description(expr, attrs={}) source code
 
hsp(expr, attrs={}) source code
 
hsp_value(expr, attrs={}) source code
 
hsp_frame(expr, attrs={}) source code
 
hsp_strand(expr, attrs={}) source code
 
hsp_seqalign_query_seq(expr, attrs={}) source code
 
hsp_seqalign_homology_seq(expr, attrs={}) source code
 
hsp_seqalign_subject_seq(expr, attrs={}) source code
 
hsp_seqalign_query_leader(expr, attrs={}) source code
 
hsp_seqalign_query_name(expr, attrs={}) source code
 
hsp_seqalign_subject_name(expr, attrs={}) source code
 
hsp_seqalign(expr, attrs={}) source code
 
hsp_seqalign_query_start(expr, attrs={}) source code
 
hsp_seqalign_query_end(expr, attrs={}) source code
 
hsp_seqalign_subject_start(expr, attrs={}) source code
 
hsp_seqalign_subject_end(expr, attrs={}) source code
 
search_parameter(expr, attrs={}) source code
 
search_statistic(expr, attrs={}) source code
Variables [hide private]
  namespace = 'bioformat'
  NS = 'bioformat:'
  XMLNS = 'http://biopython.org/bioformat'
  _use_hack = 0
  __warningregistry__ = {('Martel and those parts of Biopython d...
Variables Details [hide private]

__warningregistry__

Value:
{('Martel and those parts of Biopython depending on it directly (such \
as Bio.Mindy and Bio.Std) are now deprecated, and will be removed in a\
 future release of Biopython.  If you want to continue to use this cod\
e, please get in contact with the Biopython developers via the mailing\
 lists to avoid its permanent removal from Biopython.',
  <type 'exceptions.DeprecationWarning'>,
  18): 1}