Module Expr Str ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam defaults body Return Call NameLoad AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Return AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr NameLoad decorator_list Assign NameStore Call NameLoad NameLoad NameLoad decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body If NameLoad body Assign AttributeStore NameLoad attr BinOpAdd BinOpAdd NameLoad Str NameLoad orelse Assign AttributeStore NameLoad attr NameLoad decorator_list decorator_list ClassDef bases body Expr Str FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr Str Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr Num decorator_list FunctionDef arguments args NameParam defaults body Return Call AttributeLoad Str attr Call NameLoad NameLoad TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr BinOpAdd AttributeLoad NameLoad attr Num AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body If CompareEq Call NameLoad NameLoad Num body Assign TupleStore AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr NameLoad Assign TupleStore AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr AttributeStore NameLoad attr Call NameLoad NameLoad TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AugAssignSub AttributeStore NameLoad attr Num decorator_list decorator_list FunctionDef arguments args NameParam defaults body Expr Str While Num body Assign NameStore Call AttributeLoad NameLoad attr If UnaryOpNot NameLoad body Raise NameLoad If CompareEq SubscriptLoad NameLoad Index Num Str body Continue If Call AttributeLoad NameLoad attr Str body Continue Assign NameStore Call NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad SubscriptLoad NameLoad Slice Num attr Expr Yield NameLoad decorator_list
N/A N/A 
Maq.py - Working with Maq formatted files
=========================================

This module provides a parser for the output of the maq mapper.
As this mapper is out of use, the contents here are of historical
interest only.

Reference
---------

 Error N/A Exception N/A N/A Base class for exceptions in this module. __str__ N/A N/A self N/A N/A N/A N/A str N/A self message N/A _get_message N/A N/A self message N/A N/A N/A N/A self _message N/A _set_message N/A N/A self message N/A N/A N/A N/A self _message message N/A N/A message N/A property _get_message _set_message N/A ParsingError N/A Error N/A N/A Exception raised for errors while parsing

    Attributes:
        message -- explanation of the error
     __init__ N/A N/A self message line N/A None N/A N/A line N/A N/A N/A self message N/A N/A message  at line: line N/A N/A N/A self message message N/A N/A Match N/A N/A N/A a maq match.
     __init__ N/A N/A self N/A N/A N/A N/A self mName None N/A N/A self contig None N/A N/A self start 0 N/A N/A self strand + N/A N/A self mPairInsert 0 N/A N/A self mPairFlag 0 N/A N/A self mQuality 0 N/A N/A self mQualitySingle 0 N/A N/A self mQualityAlternative 0 N/A N/A self mNMismatches 0 N/A N/A self mMismatchQuality 0 N/A N/A self mNMismatch0 0 N/A N/A self mNMismatch1 0 N/A N/A self mLength 0 N/A __str__ N/A N/A self N/A N/A N/A N/A N/A join N/A map str N/A N/A self mName N/A self contig N/A N/A self start 1 N/A self strand N/A self mPairInsert N/A self mPairFlag N/A self mQuality N/A self mQualitySingle N/A self mQualityAlternative N/A self mNMismatches N/A self mMismatchQuality N/A self mNMismatch0 N/A self mNMismatch1 N/A self mLength N/A fromTable N/A N/A self data N/A N/A N/A N/A N/A len data 14 N/A N/A N/A N/A self mName N/A self contig N/A self start N/A self strand N/A self mPairInsert N/A self mPairFlag N/A self mQuality N/A self mQualitySingle N/A self mQualityAlternative N/A self mNMismatches N/A self mMismatchQuality N/A self mNMismatches0 N/A self mNMismatches1 N/A self mLength data N/A N/A N/A self start N/A self mPairInsert N/A self mPairFlag N/A self mQuality N/A self mQualitySingle N/A self mQualityAlternative N/A self mNMismatches N/A self mMismatchQuality N/A self mNMismatches0 N/A self mNMismatches1 N/A self mLength N/A map int N/A N/A self start N/A self mPairInsert N/A self mPairFlag N/A self mQuality N/A self mQualitySingle N/A self mQualityAlternative N/A self mNMismatches N/A self mMismatchQuality N/A self mNMismatches0 N/A self mNMismatches1 N/A self mLength N/A N/A self start 1 N/A N/A iterator N/A N/A infile N/A N/A N/A iterate over the contents of a maq file.
     N/A 1 N/A N/A line N/A N/A infile readline N/A N/A line N/A N/A StopIteration N/A N/A N/A line N/A 0 # N/A N/A N/A N/A N/A line startswith read	contig N/A N/A N/A match N/A Match N/A N/A N/A match fromTable N/A N/A N/A line N/A -1 split N/A N/A match N/A