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python-biopython  1.60
Public Member Functions | Public Attributes
Bio.Compass.Record Class Reference

List of all members.

Public Member Functions

def __init__
def query_coverage
def hit_coverage

Public Attributes

 query
 hit
 gap_threshold
 query_length
 query_filtered_length
 query_nseqs
 query_neffseqs
 hit_length
 hit_filtered_length
 hit_nseqs
 hit_neffseqs
 sw_score
 evalue
 query_start
 hit_start
 query_aln
 hit_aln
 positives

Detailed Description

Hold information from one compass hit.
Ali1 one is the query, Ali2 the hit.

Definition at line 96 of file __init__.py.


Constructor & Destructor Documentation

Definition at line 102 of file __init__.py.

00102 
00103     def __init__(self):
00104         self.query=''
00105         self.hit=''
00106         self.gap_threshold=0
00107         self.query_length=0
00108         self.query_filtered_length=0
00109         self.query_nseqs=0
00110         self.query_neffseqs=0
00111         self.hit_length=0
00112         self.hit_filtered_length=0
00113         self.hit_nseqs=0
00114         self.hit_neffseqs=0
00115         self.sw_score=0
00116         self.evalue=-1
00117         self.query_start=-1
00118         self.hit_start=-1
00119         self.query_aln=''
00120         self.hit_aln=''
00121         self.positives=''
00122 

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Member Function Documentation

Return the length of the hit covered in the alignment

Definition at line 128 of file __init__.py.

00128 
00129     def hit_coverage(self):
00130         """Return the length of the hit covered in the alignment"""
00131         s = self.hit_aln.replace("=", "")
00132         return len(s)
00133 
00134 # Everything below is private

Return the length of the query covered in alignment

Definition at line 123 of file __init__.py.

00123 
00124     def query_coverage(self):
00125         """Return the length of the query covered in alignment"""
00126         s = self.query_aln.replace("=", "")
00127         return len(s)


Member Data Documentation

Definition at line 115 of file __init__.py.

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Definition at line 110 of file __init__.py.

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Definition at line 103 of file __init__.py.

Definition at line 118 of file __init__.py.

Definition at line 107 of file __init__.py.

Definition at line 106 of file __init__.py.

Definition at line 109 of file __init__.py.

Definition at line 108 of file __init__.py.

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Definition at line 114 of file __init__.py.


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