CloneSet58


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Clone
Mass
Clones in
CloneSet
Parameter
Count
Clone
Similarity
Syntax Category
[Sequence Length]
84220.985file_input_element_list[2]
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
18425
Bio/SwissProt/__init__.py
28384
Bio/SwissProt/SProt.py
Clone Instance
1
Line Count
84
Source Line
25
Source File
Bio/SwissProt/__init__.py

class Record: 
     """Holds information from a SwissProt record.

    Members:
    entry_name        Name of this entry, e.g. RL1_ECOLI.
    data_class        Either 'STANDARD' or 'PRELIMINARY'.
    molecule_type     Type of molecule, 'PRT',
    sequence_length   Number of residues.

    accessions        List of the accession numbers, e.g. ['P00321']
    created           A tuple of (date, release).
    sequence_update   A tuple of (date, release).
    annotation_update A tuple of (date, release).

    description       Free-format description.
    gene_name         Gene name.  See userman.txt for description.
    organism          The source of the sequence.
    organelle         The origin of the sequence.
    organism_classification  The taxonomy classification.  List of strings.
                             (http://www.ncbi.nlm.nih.gov/Taxonomy/)
    taxonomy_id       A list of NCBI taxonomy id's.
    host_organism     A list of NCBI taxonomy id's of the hosts of a virus,
                      if any.
    references        List of Reference objects.
    comments          List of strings.
    cross_references  List of tuples (db, id1[, id2][, id3]).  See the docs.
    keywords          List of the keywords.
    features          List of tuples (key name, from, to, description).
                      from and to can be either integers for the residue
                      numbers, '<', '>', or '?'

    seqinfo           tuple of (length, molecular weight, CRC32 value)
    sequence          The sequence.
    
    """ 

     def __init__(self): 
          self.entry_name = None 
          self.data_class = None 
          self.molecule_type = None 
          self.sequence_length = None 

          self.accessions = [ ] 
          self.created = None 
          self.sequence_update = None 
          self.annotation_update = None 

          self.description = [ ] 
          self.gene_name = "" 
          self.organism = [ ] 
          self.organelle = "" 
          self.organism_classification = [ ] 
          self.taxonomy_id = [ ] 
          self.host_organism = [ ] 
          self.references = [ ] 
          self.comments = [ ] 
          self.cross_references = [ ] 
          self.keywords = [ ] 
          self.features = [ ] 

          self.seqinfo = None 
          self.sequence = "" 
     

class Reference: 
     """Holds information from one reference in a SwissProt entry.

    Members:
    number      Number of reference in an entry.
    positions   Describes extent of work.  list of strings.
    comments    Comments.  List of (token, text).
    references  References.  List of (dbname, identifier)
    authors     The authors of the work.
    title       Title of the work.
    location    A citation for the work.
    
    """ 

     def __init__(self): 
          self.number = None 
          self.positions = [ ] 
          self.comments = [ ] 
          self.references = [ ] 
          self.authors = [ ] 
          self.title = [ ] 
          self.location = [ ] 
     


Clone Instance
2
Line Count
83
Source Line
84
Source File
Bio/SwissProt/SProt.py

class Record: 
     """Holds information from a SwissProt record.

    Members:
    entry_name        Name of this entry, e.g. RL1_ECOLI.
    data_class        Either 'STANDARD' or 'PRELIMINARY'.
    molecule_type     Type of molecule, 'PRT',
    sequence_length   Number of residues.

    accessions        List of the accession numbers, e.g. ['P00321']
    created           A tuple of (date, release).
    sequence_update   A tuple of (date, release).
    annotation_update A tuple of (date, release).

    description       Free-format description.
    gene_name         Gene name.  See userman.txt for description.
    organism          The source of the sequence.
    organelle         The origin of the sequence.
    organism_classification  The taxonomy classification.  List of strings.
                             (http://www.ncbi.nlm.nih.gov/Taxonomy/)
    taxonomy_id       A list of NCBI taxonomy id's.
    host_organism     A list of NCBI taxonomy id's of the hosts of a virus,
                      if any.
    references        List of Reference objects.
    comments          List of strings.
    cross_references  List of tuples (db, id1[, id2][, id3]).  See the docs.
    keywords          List of the keywords.
    features          List of tuples (key name, from, to, description).
                      from and to can be either integers for the residue
                      numbers, '<', '>', or '?'

    seqinfo           tuple of (length, molecular weight, CRC32 value)
    sequence          The sequence.
    
    """ 

     def __init__(self): 
          self.entry_name = None 
          self.data_class = None 
          self.molecule_type = None 
          self.sequence_length = None 

          self.accessions = [ ] 
          self.created = None 
          self.sequence_update = None 
          self.annotation_update = None 

          self.description = "" 
          self.gene_name = "" 
          self.organism = "" 
          self.organelle = "" 
          self.organism_classification = [ ] 
          self.taxonomy_id = [ ] 
          self.host_organism = [ ] 
          self.references = [ ] 
          self.comments = [ ] 
          self.cross_references = [ ] 
          self.keywords = [ ] 
          self.features = [ ] 

          self.seqinfo = None 
          self.sequence = "" 
     

class Reference: 
     """Holds information from 1 references in a SwissProt entry.

    Members:
    number      Number of reference in an entry.
    positions   Describes extent of work.  list of strings.
    comments    Comments.  List of (token, text).
    references  References.  List of (dbname, identifier)
    authors     The authors of the work.
    title       Title of the work.
    location    A citation for the work.
    
    """ 

     def __init__(self): 
          self.number = None 
          self.positions = [ ] 
          self.comments = [ ] 
          self.references = [ ] 
          self.authors = "" 
          self.title = "" 
          self.location = "" 
     


Clone AbstractionParameter Count: 2Parameter Bindings

class Record:
  """Holds information from a SwissProt record.

    Members:
    entry_name        Name of this entry, e.g. RL1_ECOLI.
    data_class        Either 'STANDARD' or 'PRELIMINARY'.
    molecule_type     Type of molecule, 'PRT',
    sequence_length   Number of residues.

    accessions        List of the accession numbers, e.g. ['P00321']
    created           A tuple of (date, release).
    sequence_update   A tuple of (date, release).
    annotation_update A tuple of (date, release).

    description       Free-format description.
    gene_name         Gene name.  See userman.txt for description.
    organism          The source of the sequence.
    organelle         The origin of the sequence.
    organism_classification  The taxonomy classification.  List of strings.
                             (http://www.ncbi.nlm.nih.gov/Taxonomy/)
    taxonomy_id       A list of NCBI taxonomy id's.
    host_organism     A list of NCBI taxonomy id's of the hosts of a virus,
                      if any.
    references        List of Reference objects.
    comments          List of strings.
    cross_references  List of tuples (db, id1[, id2][, id3]).  See the docs.
    keywords          List of the keywords.
    features          List of tuples (key name, from, to, description).
                      from and to can be either integers for the residue
                      numbers, '<', '>', or '?'

    seqinfo           tuple of (length, molecular weight, CRC32 value)
    sequence          The sequence.
    
    """ 

  def __init__(self):
  
    self.entry_name = None 
    self.data_class = None 
    self.molecule_type = None 
    self.sequence_length = None 
    self.accessions = [ ] 
    self.created = None 
    self.sequence_update = None 
    self.annotation_update = None 
    self.description = [[#variable605deaa0]]
    self.gene_name = "" 
    self.organism = [[#variable605deaa0]]
    self.organelle = "" 
    self.organism_classification = [ ] 
    self.taxonomy_id = [ ] 
    self.host_organism = [ ] 
    self.references = [ ] 
    self.comments = [ ] 
    self.cross_references = [ ] 
    self.keywords = [ ] 
    self.features = [ ] 
    self.seqinfo = None 
    self.sequence = "" 
  

class Reference:
   [[#variable605de980]]

  def __init__(self):
  
    self.number = None 
    self.positions = [ ] 
    self.comments = [ ] 
    self.references = [ ] 
    self.authors = [[#variable605deaa0]]
    self.title = [[#variable605deaa0]]
    self.location = [[#variable605deaa0]]
  
 

CloneAbstraction
Parameter Bindings
Parameter
Index
Clone
Instance
Parameter
Name
Value
11[[#605deaa0]]
[ ] 
12[[#605deaa0]]
"" 
21[[#605de980]]
"""Holds information from one reference in a SwissProt entry.

    Members:
    number      Number of reference in an entry.
    positions   Describes extent of work.  list of strings.
    comments    Comments.  List of (token, text).
    references  References.  List of (dbname, identifier)
    authors     The authors of the work.
    title       Title of the work.
    location    A citation for the work.
    
    """ 
22[[#605de980]]
"""Holds information from 1 references in a SwissProt entry.

    Members:
    number      Number of reference in an entry.
    positions   Describes extent of work.  list of strings.
    comments    Comments.  List of (token, text).
    references  References.  List of (dbname, identifier)
    authors     The authors of the work.
    title       Title of the work.
    location    A citation for the work.
    
    """