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_to_karyotype([record])



In [3]:

    
print(karyotype)









    



chr - NC_000913.3 NC_000913 1 4641652 white

Load PaxDb Dataset



In [4]:

    
from pyrcos.datasets import protein_abundance



In [5]:

    
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 [6]:

    
from pyrcos.objects import Circos, Heatmap, Ideogram



In [7]:

    
heatmap = Heatmap(abundance_file, "1.02r", "1.07r")
circos = Circos(karyotype, plots=heatmap, circos_path="/Users/joao/Documents/circos-0.67-7/")



In [8]:

    
circos._repr_html_









    











    Out[8]:





''



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