Package goby :: Module Reads :: Class ReadsReader
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Class ReadsReader

source code

object --+
         |
        ReadsReader

Reads sequence "reads" written in the Goby "compact" format. The ReadsReader is actually an iterator over indiviual read entries stored in the file.

Instance Methods [hide private]
 
__init__(self, filename, verbose=False)
Initialize the ReadsReader using the name of the compact file.
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next(self)
Return next read entry from the file.
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__iter__(self) source code
 
__str__(self)
str(x)
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Class Variables [hide private]
  filename = None
name of the compact reads file
  entries_reader = None
reader for the read entries (interally stored in chunks)
  entries = []
Current chunk of read entries
  current_entry_index = 0
current entry index
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, filename, verbose=False)
(Constructor)

source code 

Initialize the ReadsReader using the name of the compact file. Goby compact reads have the extension ".compact-reads"

Overrides: object.__init__

__str__(self)
(Informal representation operator)

source code 

str(x)

Overrides: object.__str__
(inherited documentation)