Package Bio :: Package AlignIO :: Module StockholmIO :: Class StockholmWriter
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Class StockholmWriter

source code

                      object --+        
                               |        
      Interfaces.AlignmentWriter --+    
                                   |    
Interfaces.SequentialAlignmentWriter --+
                                       |
                                      StockholmWriter

Stockholm/PFAM alignment writer.

Instance Methods [hide private]
 
write_alignment(self, alignment)
Use this to write (another) single alignment to an open file.
source code
 
_write_record(self, record)
Write a single SeqRecord to the file
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Inherited from Interfaces.SequentialAlignmentWriter: __init__, write_file, write_footer, write_header

Inherited from Interfaces.AlignmentWriter: clean

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables [hide private]
  pfam_gr_mapping = {'active_site': 'AS', 'intron': 'IN', 'ligan...
  pfam_gs_mapping = {'look': 'LO', 'organism': 'OS', 'organism_c...
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

write_alignment(self, alignment)

source code 

Use this to write (another) single alignment to an open file.

Note that sequences and their annotation are recorded together (rather than having a block of annotation followed by a block of aligned sequences).

Overrides: Interfaces.SequentialAlignmentWriter.write_alignment

Class Variable Details [hide private]

pfam_gr_mapping

Value:
{'active_site': 'AS',
 'intron': 'IN',
 'ligand_binding': 'LI',
 'posterior_probability': 'PP',
 'secondary_structure': 'SS',
 'surface_accessibility': 'SA',
 'transmembrane': 'TM'}

pfam_gs_mapping

Value:
{'look': 'LO', 'organism': 'OS', 'organism_classification': 'OC'}