def main():
a = get_arguments()
BRENDA_PARSER = BrendaParser()
cutoff = a.cutoff
anz = a.number
search = a.subtree
dir_search = make_dir(search)
enzyme_list = new_enzyme_list(BRENDA_PARSER)
enzym_selection = select(enzyme_list, search)
if get_structure_files(BRENDA_PARSER, enzym_selection, anz, cutoff,
dir_search):
print("SUCCESS: Structures found and downloaded")
else:
print("ERROR: Not enough processible structures available")
def main():
a = get_arguments()
BRENDA_PARSER = BrendaParser()
cutoff = snakemake.input[2]
anz = snakemake.input[1]
search = snakemake.input[0]
output = snakemake.output[0]
dir_search = make_dir(search, output)
enzyme_list = new_enzyme_list(BRENDA_PARSER)
enzym_selection = select(enzyme_list, search)
if get_structure_files(enzym_selection,anz,cutoff,dir_search,BRENDA_PARSER):
print("SUCCESS: Structures found and downloaded")
else:
print("ERROR: Not enough processible structures available")
def main():
a = get_arguments()
BRENDA_PARSER = BrendaParser()
cutoff = a.cutoff
anz = a.number
search = a.subtree
output = a.output
dir_search = make_dir(search, output)
enzyme_list = new_enzyme_list(BRENDA_PARSER)
enzym_selection = select(enzyme_list, search)
get_structure_files(enzym_selection, anz, cutoff, dir_search,
BRENDA_PARSER)
print("habe fertig!")
def main():
BRENDA_PARSER = BrendaParser()
numbers =[]
a = get_arguments()
cutoff = a.cutoff
anz = a.number
for ec in BRENDA_PARSER.keys():
n = str(ec).split(".")
if len(n)<4:
continue
new = f"{n[0]}.{n[1]}.{n[2]}"
if new not in numbers:
numbers.append(new)
f = open("config.txt", "w")
for i in numbers:
f.write(f"{i}\t{cutoff}\t{anz}\n")
f.close()
def test_parsing():
brenda = BrendaParser()
assert brenda
assert "1.1.1.1" in brenda.ec_text
def test_parsing_from_file():
brenda = BrendaParser(brenda_file=BRENDA_FILE)
assert brenda
assert "1.1.1.1" in brenda.ec_text
import pytest
import logging
from brendapy import BrendaParser, BrendaProtein
from brendapy.settings import BRENDA_FILE
BRENDA_PARSER = BrendaParser()
def test_parsing():
brenda = BrendaParser()
assert brenda
assert "1.1.1.1" in brenda.ec_text
def test_parsing_from_file():
brenda = BrendaParser(brenda_file=BRENDA_FILE)
assert brenda
assert "1.1.1.1" in brenda.ec_text
def test_protein1():
""" Test the proteinBRENDA module """
ec = "1.1.1.1"
proteins = BRENDA_PARSER.get_proteins(ec)
assert proteins
assert len(proteins) == 167
def test_protein_detail1():
proteins = BRENDA_PARSER.get_proteins(ec="1.1.1.1")
protein = proteins[1]
import csv
import libsbml
import re
from statistics import median
import sys
# to get information out of brenda:
from brendapy import BrendaParser
# to calculate the geometric mean in an easy way
from scipy.stats.mstats import gmean
import pickle
from ipywidgets.widgets.interaction import empty
BRENDA_PARSER = BrendaParser() # reuse parser
def main():
# go to directory containing the xml files
# TODO: make path relative
project_dir = '/Users/medeafux/Desktop/ETH/Masterarbeit/enzyme_cost'
model_dir = '/Users/medeafux/Desktop/ETH/Masterarbeit//Bacterial-RBA-models/Escherichia-coli-K12-WT'
os.chdir(model_dir)
# extract composition of all macrocomponents and save them as a list (?) of macromolecules (class)
tree = etree.parse("proteins.xml")
root = tree.getroot()
# get to the list of Macromolecules