Harvard:Biophysics 101/Notebook:HH/2007-2-6: Difference between revisions
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[[Harvard:Biophysics_101/2007/02/01|Assigned on Feb 1, 2007 | [[Harvard:Biophysics_101/2007/02/01|Assigned on Feb 1, 2007]] | ||
<pre> | <pre> |
Revision as of 13:40, 7 February 2007
#!/usr/bin/env python from Bio import GenBank, Seq # We can create a GenBank object that will parse a raw record # This facilitates extracting specific information from the sequences record_parser = GenBank.FeatureParser() # NCBIDictionary is an interface to Genbank ncbi_dict = GenBank.NCBIDictionary('nucleotide', 'genbank', parser = record_parser) # If you pass NCBIDictionary a GenBank id, it will download that record parsed_record = ncbi_dict['116496644'] print "GenBank id:", parsed_record.id # Extract the sequence from the parsed_record s = parsed_record.seq.tostring() print "total sequence length:", len(s) max_repeat = 9 print "method 1" for i in range(max_repeat): substr = ''.join(['T' for n in range(i+1)]) print substr, s.count(substr) print "\nmethod 2" for i in range(max_repeat): substr = ''.join(['T' for n in range(i+1)]) count = 0 pos = s.find(substr,0) while not pos == -1: count = count + 1 pos = s.find(substr,pos+1) print substr, count