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python-biopython  1.60
Public Member Functions | Public Attributes | Private Member Functions
Bio.UniGene.SequenceLine Class Reference

List of all members.

Public Member Functions

def __init__
def __repr__

Public Attributes

 acc
 nid
 lid
 pid
 clone
 image
 is_image
 end
 mgc
 seqtype
 trace
 text

Private Member Functions

def _init_from_text

Detailed Description

Store the information for one SEQUENCE line from a Unigene file

Initialize with the text part of the SEQUENCE line, or nothing.

Attributes and descriptions (access as LOWER CASE)
ACC=         GenBank/EMBL/DDBJ accession number of sequence
NID=         Unique nucleotide sequence identifier (gi)
PID=         Unique protein sequence identifier (used for non-ESTs)
CLONE=       Clone identifier (used for ESTs only)
END=         End (5'/3') of clone insert read (used for ESTs only) 
LID=         Library ID; see Hs.lib.info for library name and tissue
MGC=         5' CDS-completeness indicator; if present, 
             the clone associated with this sequence  
             is believed CDS-complete. A value greater than 511
             is the gi of the CDS-complete mRNA matched by the EST,
             otherwise the value is an indicator of the reliability
             of the test indicating CDS completeness;
             higher values indicate more reliable CDS-completeness
             predictions. 
SEQTYPE=     Description of the nucleotide sequence. Possible values
             are mRNA, EST and HTC.
TRACE=       The Trace ID of the EST sequence, as provided by NCBI
             Trace Archive

Definition at line 81 of file __init__.py.


Constructor & Destructor Documentation

def Bio.UniGene.SequenceLine.__init__ (   self,
  text = None 
)

Definition at line 107 of file __init__.py.

00107 
00108     def __init__(self,text=None):
00109         self.acc = ''
00110         self.nid = ''
00111         self.lid = ''
00112         self.pid = ''
00113         self.clone = ''
00114         self.image = ''
00115         self.is_image = False
00116         self.end = ''
00117         self.mgc = ''
00118         self.seqtype = ''
00119         self.trace = ''
00120         if not text==None:
00121             self.text=text
00122             self._init_from_text(text)


Member Function Documentation

Definition at line 133 of file __init__.py.

00133 
00134     def __repr__(self):
00135         return self.text
00136         

def Bio.UniGene.SequenceLine._init_from_text (   self,
  text 
) [private]

Definition at line 123 of file __init__.py.

00123 
00124     def _init_from_text(self,text):
00125         parts = text.split('; ');
00126         for part in parts:
00127             key, val = part.split("=")
00128             if key=='CLONE':
00129                 if val[:5]=='IMAGE':
00130                     self.is_image=True
00131                     self.image = val[6:]
00132             setattr(self,key.lower(),val)


Member Data Documentation

Definition at line 108 of file __init__.py.

Definition at line 112 of file __init__.py.

Definition at line 115 of file __init__.py.

Definition at line 113 of file __init__.py.

Definition at line 114 of file __init__.py.

Definition at line 110 of file __init__.py.

Definition at line 116 of file __init__.py.

Definition at line 109 of file __init__.py.

Definition at line 111 of file __init__.py.

Definition at line 117 of file __init__.py.

Definition at line 120 of file __init__.py.

Definition at line 118 of file __init__.py.


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