Package Bio :: Module ParserSupport
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Module ParserSupport

source code

Code to support writing parsers (DEPRECATED).

Classes:
AbstractParser         Base class for parsers.
AbstractConsumer       Base class of all Consumers.
TaggingConsumer        Consumer that tags output with its event.  For debugging
EventGenerator         Generate Biopython Events from Martel XML output
                       (note that Martel has been removed)

Functions:
safe_readline          Read a line from a handle, with check for EOF.
safe_peekline          Peek at next line, with check for EOF.
read_and_call          Read a line from a handle and pass it to a method.
read_and_call_while    Read many lines, as long as a condition is met.
read_and_call_until    Read many lines, until a condition is met.
attempt_read_and_call  Like read_and_call, but forgiving of errors.
is_blank_line          Test whether a line is blank.

Classes [hide private]
  AbstractParser
Base class for other parsers.
  AbstractConsumer
Base class for other Consumers.
  TaggingConsumer
A Consumer that tags the data stream with the event and prints it to a handle.
  EventGenerator
Handler to generate events associated with a Martel parsed file.
Functions [hide private]
 
read_and_call(uhandle, method, **keywds)
read_and_call(uhandle, method[, start][, end][, contains][, blank][, has_re])
source code
 
read_and_call_while(uhandle, method, **keywds)
read_and_call_while(uhandle, method[, start][, end][, contains][, blank][, has_re]) -> number of lines
source code
number of lines

read_and_call_until(uhandle, method, start=None, end=None, contains=None, blank=None)
Read a line from uhandle and pass it to the method until some condition is true.
source code
boolean

attempt_read_and_call(uhandle, method, **keywds)
Similar to read_and_call, but returns a boolean specifying whether the line has passed the checks.
source code
 
_fails_conditions(line, start=None, end=None, contains=None, blank=None, has_re=None) source code
boolean

is_blank_line(line, allow_spaces=0)
Return whether a line is blank.
source code
line

safe_readline(handle)
Read a line from an UndoHandle and return it.
source code
line

safe_peekline(handle)
Peek at the next line in an UndoHandle and return it.
source code
Variables [hide private]
  xml_support = 1
  __package__ = 'Bio'
  __warningregistry__ = {('Bio.ParserSupport is now deprecated w...
Function Details [hide private]

read_and_call(uhandle, method, **keywds)

source code 
read_and_call(uhandle, method[, start][, end][, contains][, blank][, has_re])

Read a line from uhandle, check it, and pass it to the method.
Raises a ValueError if the line does not pass the checks.

start, end, contains, blank, and has_re specify optional conditions
that the line must pass.  start and end specifies what the line must
begin or end with (not counting EOL characters).  contains
specifies a substring that must be found in the line.  If blank
is a true value, then the line must be blank.  has_re should be
a regular expression object with a pattern that the line must match
somewhere.

read_and_call_while(uhandle, method, **keywds)

source code 
read_and_call_while(uhandle, method[, start][, end][, contains][, blank][, has_re]) -> number of lines

Read a line from uhandle and pass it to the method as long as
some condition is true.  Returns the number of lines that were read.

See the docstring for read_and_call for a description of the parameters.

read_and_call_until(uhandle, method, start=None, end=None, contains=None, blank=None)

source code 
Read a line from uhandle and pass it to the method until
some condition is true.  Returns the number of lines that were read.

See the docstring for read_and_call for a description of the parameters.

Returns:
number of lines

attempt_read_and_call(uhandle, method, **keywds)

source code 
Similar to read_and_call, but returns a boolean specifying
whether the line has passed the checks.  Does not raise
exceptions.

See docs for read_and_call for a description of the function
arguments.

Returns:
boolean

is_blank_line(line, allow_spaces=0)

source code 
Return whether a line is blank.  allow_spaces specifies whether to
allow whitespaces in a blank line.  A true value signifies that a
line containing whitespaces as well as end-of-line characters
should be considered blank.

Returns:
boolean

safe_readline(handle)

source code 
Read a line from an UndoHandle and return it.  If there are no more
lines to read, I will raise a ValueError.

Returns:
line

safe_peekline(handle)

source code 
Peek at the next line in an UndoHandle and return it.  If there are no
more lines to peek, I will raise a ValueError.

Returns:
line


Variables Details [hide private]

__warningregistry__

Value:
{('Bio.ParserSupport is now deprecated will be removed in a future rel\
ease of Biopython.',
  <class 'Bio.BiopythonDeprecationWarning'>,
  29): True}