In [1]:

    

from pyrcos import utils
from Bio import SeqIO


    

In [2]:

    

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


    

In [3]:

    

print(karyotype)


    

    




chr - NC_000913.3 NC_000913 1 4641652 white

In [4]:

    

from pyrcos.datasets import regulatory_network


    

In [5]:

    

interactions = regulatory_network.parse_regulondb("../data/GeneProductSet.txt", 
                                                  "../data/TFSet.txt",
                                                  "../data/network_tf_gene.txt")


    

    




ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'SROD'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'SROD'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'EFEU_2'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'SGRT'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'YEGZ'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'FNRS'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'SROD'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'SROC'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'ILVG_1'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'ILVG_1'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'ILVG_2'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'ILVG_2'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'MOLR_1'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'ILVG_1'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'ILVG_2'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'MNTS'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'PHNE_2'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'MOLR_1'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'SGRT'
ERROR:/Users/joao/PycharmProjects/pyrcos/pyrcos/datasets/regulatory_network.pyc:'SROA'

In [6]:

    

positions = {f.qualifiers["locus_tag"][0]: [f.location.start, f.location.end, record.id] 
             for f in record.features if f.type == "gene"}
interactions_file = regulatory_network.convert_interactions_to_links(interactions, positions)
interactions_file.flush()


    

In [7]:

    

from pyrcos.objects import Circos, Link


    

In [8]:

    

link = Link(file=interactions_file, radius="0.98r")
circos = Circos(karyotype, links=link, circos_path="/Users/joao/Documents/circos-0.67-7/")


    

In [9]:

    

circos


    

    













    
Out[9]:





''

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