Load genome from genbank and create Karyotype



In [1]:

    
from pyrcos import utils
from Bio import SeqIO



In [2]:

    
record = SeqIO.read("../data/MG1655.gb", "gb")
karyotype = utils.convert_seq_records([record], feature_types=[])



In [3]:

    
print(karyotype)









    



chr - NC_000913.3 NC_000913 0 4641652 white

Load PaxDb Dataset



In [4]:

    
from pyrcos.datasets import protein_abundance



In [37]:

    
abundance = protein_abundance.read_paxdb("../data/paxdb.ecoli.integrated.txt")
positions = {f.qualifiers["locus_tag"][0]: [f.location.start, f.location.end, record.id] 
             for f in record.features if f.type == "gene"}

abundance_file = protein_abundance.convert_abundance_to_file(abundance, positions)

Create circos objects



In [20]:

    
from pyrcos.objects import Circos, Heatmap, Ideogram



In [33]:

    
heatmap = Heatmap(abundance_file, "1.1r", "1.15r")
circos = Circos(karyotype, plots=heatmap, circos_path="/Users/joao/Documents/circos-0.67-7/")



In [34]:

    
circos









    



/Users/joao/Documents/circos-0.67-7/bin/circos -config /var/folders/l3/z9lkd79n7slblqm475s3l2vw0000gn/T/tmpL4mZ7j -svg -dir /var/folders/l3/z9lkd79n7slblqm475s3l2vw0000gn/T -file tmpaDxG5G






    











    Out[34]:





<pyrcos.objects.Circos at 0x1122adad0>



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