Package Bio :: Module ParserSupport
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Module ParserSupport

source code

Code to support writing parsers.



Classes:
AbstractParser         Base class for parsers.
AbstractConsumer       Base class of all Consumers.
TaggingConsumer        Consumer that tags output with its event.  For debugging
SGMLStrippingConsumer  Consumer that strips SGML tags from output.
EventGenerator         Generate Biopython Events from Martel XML output
                       (note that Martel is now DEPRECATED)

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.
  SGMLStrippingConsumer
A consumer that strips off SGML tags.
  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'
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