CloneSet266


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Clone
Mass
Clones in
CloneSet
Parameter
Count
Clone
Similarity
Syntax Category
[Sequence Length]
38210.995compound_stmt
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
13872
Bio/SeqIO/FastaIO.py
2271437
Bio/SeqIO/QualityIO.py
Clone Instance
1
Line Count
38
Source Line
72
Source File
Bio/SeqIO/FastaIO.py

    def __init__(self,handle,wrap = 60,record2title = None):
                                                           
        '''Create a Fasta writer.

        handle - Handle to an output file, e.g. as returned
                 by open(filename, "w")
        wrap -   Optional line length used to wrap sequence lines.
                 Defaults to wrapping the sequence at 60 characters
                 Use zero (or None) for no wrapping, giving a single
                 long line for the sequence.
        record2title - Optional function to return the text to be
                 used for the title line of each record.  By default the
                 a combination of the record.id and record.description
                 is used.  If the record.description starts with the
                 record.id, then just the record.description is used.

        You can either use:

        myWriter = FastaWriter(open(filename,"w"))
        writer.write_file(myRecords)

        Or, follow the sequential file writer system, for example:

        myWriter = FastaWriter(open(filename,"w"))
        writer.write_header() # does nothing for Fasta files
        ...
        Multiple calls to writer.write_record() and/or writer.write_records()
        ...
        writer.write_footer() # does nothing for Fasta files
        writer.close()
        ''' 
        SequentialSequenceWriter.__init__(self,handle) 
        #self.handle = handle
        self.wrap = None 
        if wrap: 
            if wrap<1:   
                raise ValueError 
            
        self.wrap = wrap 
        self.record2title = record2title 


Clone Instance
2
Line Count
27
Source Line
1437
Source File
Bio/SeqIO/QualityIO.py

    def __init__(self,handle,wrap = 60,record2title = None):
                                                           
        '''Create a QUAL writer.

        Arguments:
         - handle - Handle to an output file, e.g. as returned
                    by open(filename, "w")
         - wrap   - Optional line length used to wrap sequence lines.
                    Defaults to wrapping the sequence at 60 characters
                    Use zero (or None) for no wrapping, giving a single
                    long line for the sequence.
         - record2title - Optional function to return the text to be
                    used for the title line of each record.  By default
                    a combination of the record.id and record.description
                    is used.  If the record.description starts with the
                    record.id, then just the record.description is used.

        The record2title argument is present for consistency with the
        Bio.SeqIO.FastaIO writer class.
        ''' 
        SequentialSequenceWriter.__init__(self,handle) 
        #self.handle = handle
        self.wrap = None 
        if wrap: 
            if wrap<1:   
                raise ValueError 
            
        self.wrap = wrap 
        self.record2title = record2title 


Clone AbstractionParameter Count: 1Parameter Bindings

def __init__(self,handle,wrap = 60,record2title = None):
   [[#variable5d78dfa0]]
  SequentialSequenceWriter.__init__(self,handle) 
  #self.handle = handle
  self.wrap = None 
  if wrap:
  
    if wrap<1:
    
      raise ValueError 
    
  self.wrap = wrap 
  self.record2title = record2title 
 

CloneAbstraction
Parameter Bindings
Parameter
Index
Clone
Instance
Parameter
Name
Value
11[[#5d78dfa0]]
'''Create a Fasta writer.

        handle - Handle to an output file, e.g. as returned
                 by open(filename, "w")
        wrap -   Optional line length used to wrap sequence lines.
                 Defaults to wrapping the sequence at 60 characters
                 Use zero (or None) for no wrapping, giving a single
                 long line for the sequence.
        record2title - Optional function to return the text to be
                 used for the title line of each record.  By default the
                 a combination of the record.id and record.description
                 is used.  If the record.description starts with the
                 record.id, then just the record.description is used.

        You can either use:

        myWriter = FastaWriter(open(filename,"w"))
        writer.write_file(myRecords)

        Or, follow the sequential file writer system, for example:

        myWriter = FastaWriter(open(filename,"w"))
        writer.write_header() # does nothing for Fasta files
        ...
        Multiple calls to writer.write_record() and/or writer.write_records()
        ...
        writer.write_footer() # does nothing for Fasta files
        writer.close()
        ''' 
12[[#5d78dfa0]]
'''Create a QUAL writer.

        Arguments:
         - handle - Handle to an output file, e.g. as returned
                    by open(filename, "w")
         - wrap   - Optional line length used to wrap sequence lines.
                    Defaults to wrapping the sequence at 60 characters
                    Use zero (or None) for no wrapping, giving a single
                    long line for the sequence.
         - record2title - Optional function to return the text to be
                    used for the title line of each record.  By default
                    a combination of the record.id and record.description
                    is used.  If the record.description starts with the
                    record.id, then just the record.description is used.

        The record2title argument is present for consistency with the
        Bio.SeqIO.FastaIO writer class.
        '''