Ace contig class
Revision as of 05:07, 29 June 2009 by Davidw
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.
#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...' 1