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‎.travis.yml

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@@ -8,6 +8,7 @@ install:
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# !!! It will take 14 minutes, so response is needed. But the full output is too long !!!
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# - pip install -v scipy | grep ^.*building
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- pip install -r requirements.txt
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- apt-get install pypy
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- cd BioBLESS/biocircuit
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- make
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- python biogate_gen.py

‎backend/BioBLESS/biosys/bio_system_old.py

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#!/usr/bin/env python
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"""
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This is a module to describe BioSystem.
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There is a function named bio_system in this module.
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The format to input is in doc/api-for-front/gates_specification.txt
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Examples
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--------------
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Create some biosys to calculate their simulation
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>>> test = bio_system(data)
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>>> test.simulation()
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"""
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__author__ = 'Trumpet'
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import os
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try:
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import simplejson
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except:
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import json as simplejson
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from reaction_system import ReactionSystem
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GATE_FILE = None
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real_path = os.path.split(os.path.realpath(__file__))[0]+"/"
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try:
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GATE_FILE = open(real_path+"../../../doc/devices/gates_lizhi.json", "r")
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except IOError:
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GATE_FILE = open(real_path+"../doc/devices/gates_lizhi.json", "r")
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gate_data_source = GATE_FILE.read()
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gates_data = simplejson.loads(gate_data_source)
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gates_data = list(gates_data)
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gates_data.append({
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"id": "INPUT",
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"input": [],
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"output": ["d1"],
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"parts": {
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"id": [["d1"]],
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"type": {"d1": "Input"}
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},
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"map": [],
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"type": {}
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})
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def dev_system(gates, data, nodes_id, input_sub, output_sub):
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"""
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To build a reaction system from the data of a device.
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Input gates data(from doc/devices/gates_lizi.json),
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and data(format is the same with the system data),
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nodes_id,input_sub and output_sub(str)
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Then return a reaction system.
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This reaction system will be sumerize in bio_system
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"""
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if gates["id"] == "INPUT":
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species = [[gates["parts"]["id"][0][0], data["device_parameter"]["initial"][0]]]
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reaction = []
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else:
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def coding_find_last(tmp, string):
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while parts_type[tmp] != string:
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tmp -= 1
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return tmp + 1
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def select(list_from, string):
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ans = []
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tmp = 0
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flag = True
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while flag:
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try:
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ans.append(list_from.index(string, tmp) + 1)
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tmp = ans[-1]
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except ValueError:
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flag = False
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return ans
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def get_species(list_from, str_list):
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list_from = map(str, list_from)
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return [i + j for i in str_list for j in list_from]
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def find_in_map(tmp=0, **kw):
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for single_map in range(tmp, len(maps)):
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try:
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if maps[single_map][kw.keys()[0]] == kw.values()[0]:
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return single_map#
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except KeyError:
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pass
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return -1
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parts_type = [gates["parts"]["type"]["d" + str(i + 1)] for i in range(len(gates["parts"]["type"]))]
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maps = gates["map"]
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protein = select(parts_type, "Coding")
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s_rna = select(parts_type, "sRNA")
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species = get_species(protein, ["d", "m", "r", "l", "p"]) + get_species(s_rna, ["d", "m", "r"])
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initial = data["device_parameter"]["initial"]
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for i in range(len(initial)):
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for j in gates["parts"]["id"][i]:
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if j[0] == "d":
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try:
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species[species.index(j)] = [j, initial[i]]
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except ValueError:
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pass
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species += gates["input"]
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reaction = []
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for single in protein + s_rna:
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part_type = parts_type[single - 1]
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part_id = str(single)
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maper = find_in_map(id1="d" + part_id)
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single_data = data[maps[maper]["id"]]
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single_reaction = [
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[["d" + part_id], ["m" + part_id], single_data["trans1"]],
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[["m" + part_id], ["d" + part_id, "r" + part_id], single_data["trans1"]],
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[["r" + part_id], [], single_data["decay1"]],
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[["r" + part_id], ["l" + part_id], single_data["trans2"]],
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[["l" + part_id], ["r" + part_id, "p" + part_id], single_data["trans2"]],
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[["p" + part_id], [], single_data["decay2"]],
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] if part_type == "Coding" else [
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[["d" + part_id], ["m" + part_id], single_data["trans1"]],
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[["m" + part_id], ["d" + part_id, "r" + part_id], single_data["trans1"]],
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[["r" + part_id], [], single_data["decay1"]],
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]
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for reg_sub in ["Promoter", "RBS"]:
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#print reg_sub+","+str(single)#
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if reg_sub == "Promoter":
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pro = coding_find_last(single, reg_sub)
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tmp = find_in_map(id2="d" + str(pro))
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else:
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rbs = coding_find_last(single, reg_sub)
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if rbs > pro:
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pro = rbs
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tmp = find_in_map(id2="d" + str(pro))
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else:
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tmp = -1
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while tmp != -1:
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reg_data = data[maps[tmp]["id"]]
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reg_pro = maps[tmp]["id1"]
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#print str(maps[tmp]["id"])+","+str(reg_data)#
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"""
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d -> r -> p
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m l
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n i
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"""
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if maps[tmp]["type"] == "inh":
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single_reaction.append(
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[[reg_pro, "m" + part_id], ["n" + part_id], reg_data["reg"] * single_data["trans1"]]
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)
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single_reaction.append(
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[["n" + part_id], [reg_pro, "d" + part_id], reg_data["reg"] * single_data["trans1"]]
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)
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if not "n" + part_id in species:
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species.append("n" + part_id)
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temp = find_in_map(id2="e" + str(tmp+1))
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while temp != -1:
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rep_data = data[maps[temp]["id"]]
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rep_pro = maps[temp]["id1"]
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single_reaction.append(
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[[rep_pro, "n" + part_id], ["m" + part_id, reg_pro, rep_pro],
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rep_data["reg"] * reg_data["reg"] * single_data["trans1"]]
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)
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temp = find_in_map(temp + 1, id2="e" + str(tmp+1))
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if maps[tmp]["type"] == "lock":
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single_reaction.append(
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[[reg_pro, "l" + part_id], ["i" + part_id], reg_data["reg"] * single_data["trans2"]]
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)
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single_reaction.append(
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[["i" + part_id], [reg_pro, "r" + part_id], reg_data["reg"] * single_data["trans2"]]
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)
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if not "i" + part_id in species:
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species.append("i" + part_id)
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if maps[tmp]["type"] == "act":
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single_reaction.append(
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[[reg_pro, "d" + part_id], [reg_pro, "d" + part_id, "r" + part_id],
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reg_data["reg"] * single_data["trans1"]]
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)
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if maps[tmp]["type"] == "key":
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single_reaction.append(
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[[reg_pro, "r" + part_id], [reg_pro, "p" + part_id, "r" + part_id],
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reg_data["reg"] * single_data["trans2"]]
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)
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tmp = find_in_map(tmp + 1, id2="d" + str(pro))
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reaction += single_reaction
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def add_str(list_from, nodes_id):
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for sig in list_from:
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if isinstance(sig, list):
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add_str(sig, nodes_id)
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for sig in range(len(list_from)):
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if isinstance(list_from[sig], str) or isinstance(list_from[sig], unicode):
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list_from[sig] = nodes_id + list_from[sig]
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def replace_str(list_from, st1, st2):
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for sig in list_from:
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if isinstance(sig, list):
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replace_str(sig, st1, st2)
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for sig in range(len(list_from)):
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if list_from[sig] == st1:
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list_from[sig] = st2
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#"""
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add_str(species, "S"+nodes_id)
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add_str(reaction, "S"+nodes_id)
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tmp = [replace_str(species, "S"+nodes_id + gates["input"][i], "S"+input_sub[i]) for i in range(len(input_sub))]
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tmp = [replace_str(species, "S"+nodes_id + gates["output"][i], "S"+output_sub[i]) for i in range(len(output_sub))]
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tmp = [replace_str(reaction, "S"+nodes_id + gates["input"][i], "S"+input_sub[i]) for i in range(len(input_sub))]
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tmp = [replace_str(reaction, "S"+nodes_id + gates["output"][i], "S"+output_sub[i]) for i in range(len(output_sub))]
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"""
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add_str(species, nodes_id)
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add_str(reaction, nodes_id)
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tmp = [replace_str(species, nodes_id + gates["input"][i], input_sub[i]) for i in range(len(input_sub))]
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tmp = [replace_str(species, nodes_id + gates["output"][i], output_sub[i]) for i in range(len(output_sub))]
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tmp = [replace_str(reaction, nodes_id + gates["input"][i], input_sub[i]) for i in range(len(input_sub))]
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tmp = [replace_str(reaction, nodes_id + gates["output"][i], output_sub[i]) for i in range(len(output_sub))]
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"""
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return ReactionSystem(reaction, species)
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def bio_system(system_data):
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"""
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Input a BioSystem, and output the reaction system with simulation.
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The format to input is in doc/api-for-front/gates_specification.txt
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Input it,and return a reaction system which you can use simulation() and record_list
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"""
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time = system_data["system_parameter"]["time"]
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gates = {single_gate["id"]: single_gate for single_gate in gates_data}
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nodes = system_data["nodes"]
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devices = [dev_system(
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gates[nodes[i]],
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system_data["simulation_parameters"][i],
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str(i),
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[str(j["from"]) for j in system_data["arcs"] if j["to"] == i],
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[str(i)]
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) for i in range(len(nodes))]
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reaction = devices[0]
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for single_nodes in range(1, len(nodes)):
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reaction += devices[single_nodes]
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reaction.time = time
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reaction.nodes = nodes
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return reaction
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def json_to_json(string):
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system = bio_system(simplejson.loads(string))
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system.simulation()
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return simplejson.dumps(system.record)
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if __name__ == "__main__":
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reader = raw_input()
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print json_to_json(reader)

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