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In [8]:

    
from goetia import dbg
import screed



In [10]:

    
screed.read_fasta_sequences('/store/biodb/genomes/sacPom.pombase.fa')









    Out[10]:





<ScreedDB, '/store/biodb/genomes/sacPom.pombase.fa_screed'>



In [11]:

    
sacpom_db = screed.ScreedDB('/store/biodb/genomes/sacPom.pombase.fa')



In [5]:

    
g = dbg.ExactDBG(51)
g.consume_fastx('/store/biodb/genomes/sacPom.pombase.fa')









    



Consumed 0 reads...






    Out[5]:





2716915



In [17]:

    
s = sacpom_db['SPAC212.11|1|5662|-1|tlh1|I|protein_coding|RecQ'].sequence



In [21]:

    
max([g.kmer_degree(s[i:i+g.K]) for i in range(len(s)-g.K-1)])









    Out[21]:





3



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