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python-biopython  1.60
Public Member Functions | Public Attributes | Private Attributes
Bio.SeqIO.TabIO.TabWriter Class Reference
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List of all members.

Public Member Functions

def write_record
def write_header
def write_footer
def write_records
def write_file
def clean

Public Attributes

 handle

Private Attributes

 _record_written

Detailed Description

Class to write simple tab separated format files.

Each line consists of "id(tab)sequence" only.

Any description, name or other annotation is not recorded.

Definition at line 70 of file TabIO.py.


Member Function Documentation

def Bio.SeqIO.Interfaces.SequenceWriter.clean (   self,
  text 
) [inherited]
Use this to avoid getting newlines in the output.

Definition at line 166 of file Interfaces.py.

00166 
00167     def clean(self, text):
00168         """Use this to avoid getting newlines in the output."""
00169         return text.replace("\n", " ").replace("\r", " ").replace("  ", " ")
    

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def Bio.SeqIO.Interfaces.SequentialSequenceWriter.write_file (   self,
  records 
) [inherited]
Use this to write an entire file containing the given records.

records - A list or iterator returning SeqRecord objects

This method can only be called once.  Returns the number of records
written.

Reimplemented from Bio.SeqIO.Interfaces.SequenceWriter.

Definition at line 262 of file Interfaces.py.

00262 
00263     def write_file(self, records):
00264         """Use this to write an entire file containing the given records.
00265 
00266         records - A list or iterator returning SeqRecord objects
00267 
00268         This method can only be called once.  Returns the number of records
00269         written.
00270         """
00271         self.write_header()
00272         count = self.write_records(records)
00273         self.write_footer()
00274         return count

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Definition at line 218 of file Interfaces.py.

00218 
00219     def write_footer(self):
00220         assert self._header_written, "You must call write_header() first"
00221         assert self._record_written, "You have not called write_record() or write_records() yet"
00222         assert not self._footer_written, "You have aleady called write_footer()"
00223         self._footer_written = True

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Definition at line 212 of file Interfaces.py.

00212 
00213     def write_header(self):
00214         assert not self._header_written, "You have aleady called write_header()"
00215         assert not self._record_written, "You have aleady called write_record() or write_records()"
00216         assert not self._footer_written, "You have aleady called write_footer()"
00217         self._header_written = True
        

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def Bio.SeqIO.TabIO.TabWriter.write_record (   self,
  record 
)
Write a single tab line to the file.

Reimplemented from Bio.SeqIO.Interfaces.SequentialSequenceWriter.

Definition at line 77 of file TabIO.py.

00077 
00078     def write_record(self, record):
00079         """Write a single tab line to the file."""
00080         assert self._header_written
00081         assert not self._footer_written
00082         self._record_written = True
00083         
00084         title = self.clean(record.id)
00085         seq = self._get_seq_string(record) #Catches sequence being None
00086         assert "\t" not in title
00087         assert "\n" not in title
00088         assert "\r" not in title
00089         assert "\t" not in seq
00090         assert "\n" not in seq
00091         assert "\r" not in seq
00092         self.handle.write("%s\t%s\n" % (title, seq))
00093 

def Bio.SeqIO.Interfaces.SequentialSequenceWriter.write_records (   self,
  records 
) [inherited]
Write multiple record to the output file.

records - A list or iterator returning SeqRecord objects

Once you have called write_header() you can call write_record()
and/or write_records() as many times as needed.  Then call
write_footer() and close().

Returns the number of records written.

Definition at line 240 of file Interfaces.py.

00240 
00241     def write_records(self, records):
00242         """Write multiple record to the output file.
00243 
00244         records - A list or iterator returning SeqRecord objects
00245 
00246         Once you have called write_header() you can call write_record()
00247         and/or write_records() as many times as needed.  Then call
00248         write_footer() and close().
00249 
00250         Returns the number of records written.
00251         """
00252         #Default implementation:
00253         assert self._header_written, "You must call write_header() first"
00254         assert not self._footer_written, "You have already called write_footer()"
00255         count = 0
00256         for record in records:
00257             self.write_record(record)
00258             count += 1
00259         #Mark as true, even if there where no records
00260         self._record_written = True
00261         return count

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Member Data Documentation

Reimplemented from Bio.SeqIO.Interfaces.SequentialSequenceWriter.

Definition at line 81 of file TabIO.py.

Reimplemented from Bio.SeqIO.Interfaces.SequenceWriter.

Definition at line 207 of file Interfaces.py.


The documentation for this class was generated from the following file: