Ace contig class

This page describes the Contig class used in Bio.Sequencing.Ace to hold all of the imfomation about a single contig recored in an Ace file.

Summary Diagram

Examples

#Start my parsing a file to get some contigs 
>>>from Bio.Sequencing import Ace
>>>ace_gen = Ace.parse(open("contig1.ace", 'r')) # from Tests/Ace/contig1.ace
>>>contig = ace_gen.next()
 
# just the consensus sequence
>>>contig.sequence
'aatacgGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTG......'
# assembler designated quality for each base in the consensus
>>>contig.quality
[0, 0, 0, 0, 0, 0, 22, 23, 25, 28, 34, 47,...]
 
# Ace files also contain information on the reads that make up the consensus.
# Information about the reads are in two lists, "reads" and "af"
 
# so, to get read sequence for every read in a contig
# and that reads position in its contig
>>>for i in range(len(contig.reads)):               
...     contig.af[i].padded_start           
...     contig.reads[i].rd.sequence
...                                
'tagcgaggaaagaacccaacaGg...'
-14  
'aatacgGGATTGCCCTagtaacG...'
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