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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


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 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
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

Constructor & Destructor Documentation

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

Definition at line 107 of file

00108     def __init__(self,text=None):
00109         self.acc = ''
00110         self.nid = ''
00111         self.lid = ''
00112 = ''
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

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

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

Definition at line 123 of file

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

Definition at line 112 of file

Definition at line 115 of file

Definition at line 113 of file

Definition at line 114 of file

Definition at line 110 of file

Definition at line 116 of file

Definition at line 109 of file

Definition at line 111 of file

Definition at line 117 of file

Definition at line 120 of file

Definition at line 118 of file

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