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python-biopython  1.60
Classes | Namespaces | Functions | Variables
__init__.py File Reference

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Classes

class  Bio.GenBank.Iterator
class  Bio.GenBank.ParserFailureError
class  Bio.GenBank.LocationParserError
class  Bio.GenBank.FeatureParser
class  Bio.GenBank.RecordParser
class  Bio.GenBank._BaseGenBankConsumer
class  Bio.GenBank._FeatureConsumer
class  Bio.GenBank._RecordConsumer

Namespaces

namespace  Bio.GenBank

Functions

def Bio.GenBank._pos
def Bio.GenBank._loc
def Bio.GenBank._split_compound_loc
def Bio.GenBank.parse
def Bio.GenBank.read
def Bio.GenBank._test

Variables

int Bio.GenBank.GENBANK_INDENT = 12
string Bio.GenBank.GENBANK_SPACER = " "
int Bio.GenBank.FEATURE_KEY_INDENT = 5
int Bio.GenBank.FEATURE_QUALIFIER_INDENT = 21
string Bio.GenBank.FEATURE_KEY_SPACER = " "
string Bio.GenBank.FEATURE_QUALIFIER_SPACER = " "
string Bio.GenBank._solo_location = r"[<>]?\d+"
string Bio.GenBank._pair_location = r"[<>]?\d+\.\.[<>]?\d+"
string Bio.GenBank._between_location = r"\d+\^\d+"
string Bio.GenBank._within_position = r"\(\d+\.\d+\)"
tuple Bio.GenBank._re_within_position = re.compile(_within_position)
string Bio.GenBank._within_location = r"([<>]?\d+|%s)\.\.([<>]?\d+|%s)"
string Bio.GenBank._oneof_position = r"one\-of\(\d+(,\d+)+\)"
tuple Bio.GenBank._re_oneof_position = re.compile(_oneof_position)
string Bio.GenBank._oneof_location = r"([<>]?\d+|%s)\.\.([<>]?\d+|%s)"
string Bio.GenBank._simple_location = r"\d+\.\.\d+"
tuple Bio.GenBank._re_simple_location = re.compile(_simple_location)
tuple Bio.GenBank._re_simple_compound
string Bio.GenBank._complex_location = r"([a-zA-z][a-zA-Z0-9_]*(\.[a-zA-Z0-9]+)?\:)?(%s|%s|%s|%s|%s)"
tuple Bio.GenBank._re_complex_location = re.compile(r"^%s$" % _complex_location)
string Bio.GenBank._possibly_complemented_complex_location = r"(%s|complement\(%s\))"
tuple Bio.GenBank._re_complex_compound

Class Documentation

class Bio::GenBank::ParserFailureError
Failure caused by some kind of problem in the parser.

Definition at line 387 of file __init__.py.

class Bio::GenBank::LocationParserError
Could not Properly parse out a location from a GenBank file.

Definition at line 392 of file __init__.py.