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Commit message:
planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5 |
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modified:
rpviz.xml |
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added:
rpviz/LICENSE rpviz/README.md rpviz/Test with Ecoli ntwk/Copy_of_All_genes_of_E._coli_K-12_substr._MG1655.txt rpviz/Test with Ecoli ntwk/E coli PPI network.py rpviz/Test with Ecoli ntwk/HT.PMID-15690043.EcoliNet.303gene.3446link.txt rpviz/__init__.py rpviz/__pycache__/__init__.cpython-37.pyc rpviz/__pycache__/main.cpython-37.pyc rpviz/__pycache__/network2json.cpython-37.pyc rpviz/__pycache__/py2html2.cpython-37.pyc rpviz/__pycache__/sbml2lists.cpython-37.pyc rpviz/__pycache__/smile2picture.cpython-37.pyc rpviz/csv_network.py rpviz/images_report/node diagram.png rpviz/images_report/script diagram.png rpviz/images_report/workflow.PNG rpviz/main.py rpviz/network2json.py rpviz/new_html/cytoscape.min.js rpviz/new_html/output.html rpviz/new_html/template2.html rpviz/nxvisualizer.py rpviz/py2html2.py rpviz/sbml2lists.py rpviz/smile2picture.py |
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| diff -r 785b6253af1f -r fe78fd6b315a rpviz.xml --- a/rpviz.xml Tue Jun 11 10:03:06 2019 -0400 +++ b/rpviz.xml Tue Jun 11 11:42:40 2019 -0400 |
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| @@ -1,7 +1,7 @@ <tool id="rpviz" name="rpVisualizer" version="0.1.0" python_template_version="3.5"> <description>Pathway visualizer</description> <requirements> - <requirement type="package">python-libsbml</requirement> + <requirement type="package" version="5.18">python-libsbml</requirement> <requirement type="package">networkx</requirement> <requirement type="package">beautifulsoup4</requirement> <requirement type="package">rdkit</requirement> |
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| diff -r 785b6253af1f -r fe78fd6b315a rpviz/LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/LICENSE Tue Jun 11 11:42:40 2019 -0400 |
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| @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2019 Pablo Carbonell + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. |
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| diff -r 785b6253af1f -r fe78fd6b315a rpviz/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/README.md Tue Jun 11 11:42:40 2019 -0400 |
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| @@ -0,0 +1,18 @@ +# rpviz +Metabolic engineering visualizer + +csv_network.py : To read information from a csv file +sbml2list.py : To read information from a sbml file + +smile2picture.py : To convert SMILES into svg image + +network2json.py : To convert the network in a json file + +## 1 html/pathway +py2html : To create an html file from a json file, using a template (in html/template.html) with jinja2 and to use it with + +## 1 html updated for each pathway +py2html2 : To create a .js file with the json file and to open it with the template2 (in html/template2.html) and the network_viewer.js + +nxvisualizer.py : To open the network directly in Cytoscape + |
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| diff -r 785b6253af1f -r fe78fd6b315a rpviz/Test with Ecoli ntwk/Copy_of_All_genes_of_E._coli_K-12_substr._MG1655.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/Test with Ecoli ntwk/Copy_of_All_genes_of_E._coli_K-12_substr._MG1655.txt Tue Jun 11 11:42:40 2019 -0400 |
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| b'@@ -0,0 +1,4632 @@\n+"Gene Name"\t"Accession-1"\t"Left-End-Position"\t"Right-End-Position"\t"Product"\t"Map to Escherichia coli CFT073"\t"Accession-1"\t"Accession-1"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11979"\t"b2038"\t2109581\t2110138\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=DTDPDEHYDRHAMEPIM-MONOMER"\t""\t"b2038"\t"b2038"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11991"\t"b2112"\t2192515\t2192796\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11991-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C2640"\t"b2112"\t"b2112"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG12302"\t"b1098"\t1155124\t1155765\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=DTMPKI-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C1370"\t"b1098"\t"b1098"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG12320"\t"b0127"\t142779\t143705\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=YADG-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C0156"\t"b0127"\t"b0127"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11428"\t"b3962"\t4159390\t4160790\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=UDHA-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C4923"\t"b3962"\t"b3962"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG10649"\t"b1109"\t1166085\t1167389\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=NADH-DHII-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C1382"\t"b1109"\t"b1109"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11650"\t"b0209"\t231122\t231922\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11650-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C0246"\t"b0209"\t"b0209"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11045"\t"b3831"\t4016431\t4017192\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=URPHOS-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C4773"\t"b3831"\t"b3831"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG10818"\t"b3752"\t3937294\t3938223\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=RIBOKIN-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C4680"\t"b3752"\t"b3752"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11257"\t"b0385"\t403703\t404818\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11257-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C0492"\t"b0385"\t"b0385"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG10566"\t"b1613"\t1688576\t1689751\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=MANNPISOM-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C2005"\t"b1613"\t"b1613"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G7468"\t"b2848"\t2989304\t2989786\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G7468-MONOMER"\t""\t"b2848"\t"b2848"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG10413"\t"b3779"\t3962745\t3964229\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=PPPGPPHYDRO-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C4699"\t"b3779"\t"b3779"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG10290"\t"b4287"\t4510690\t4511457\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=FECE-MONOMER"\t""\t"b4287"\t"b4287"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG12411"\t"b2040"\t2111077\t2111976\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=DTDPDEHYRHAMREDUCT-MONOMER"\t""\t"b2040"\t"b2040"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG10468"\t"b0972"\t1032139\t1033257\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=HYAA-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C1113"\t"b0972"\t"b0972"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G7015"\t"b1843"\t1925440\t1926096\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G7015-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C2253"\t"b1843"\t"b1843"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11971"\t"b2393"\t2513042\t2514244\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=NUPC-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C2932"\t"b2393"\t"b2393"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG10053"\t"b0063"\t68348\t70048\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=RIBULOKIN-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C0075"\t"b0063"\t"b0063"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G6273"\t"b0502"\t529645\t530016\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G6273-MONOMER"\t""\t"b0502"\t"b0502"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11789"\t"b2051"\t2125743\t2126222\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=GD'..b'3989828\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=UROGENIIISYN-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C4723"\t"b3804"\t"b3804"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG30079"\t"b3758"\t3943704\t3946607\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=RRLC-RRNA"\t""\t"b3758"\t"b3758"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G7111"\t"b2072"\t2151711\t2152472\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G7111-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C2598"\t"b2072"\t"b2072"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG10039"\t"b1982"\t2055061\t2056515\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=AMP-NUCLEOSID-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C2444"\t"b1982"\t"b1982"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG10389"\t"b0809"\t845741\t846463\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=GLNQ-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C0894"\t"b0809"\t"b0809"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11198"\t"b3730"\t3913830\t3915200\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=NAG1P-URIDYLTRANS-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C4655"\t"b3730"\t"b3730"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG10931"\t"b0723"\t755907\t757673\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=SDH-FLAVO"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C0801"\t"b0723"\t"b0723"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G6843"\t"b1585"\t1656747\t1657457\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G6843-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C1975"\t"b1585"\t"b1585"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG20257"\t"b2675"\t2801348\t2803492\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=NRDE-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C3228"\t"b2675"\t"b2675"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11848"\t"b3883"\t4073739\t4074635\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11848-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C4825"\t"b3883"\t"b3883"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG10427"\t"b1210"\t1263714\t1264970\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=GLUTRNAREDUCT-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C1668"\t"b1210"\t"b1210"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG10162"\t"b2048"\t2121609\t2122979\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=PHOSMANMUT-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C2557"\t"b2048"\t"b2048"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G6424"\t"b0821"\t857796\t859061\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G6424-MONOMER"\t""\t"b0821"\t"b0821"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11102"\t"b0477"\t500125\t501429\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=GSK-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C0597"\t"b0477"\t"b0477"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G6656"\t"b1318"\t1380821\t1381789\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=YCJV-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C1790"\t"b1318"\t"b1318"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G7093"\t"b2042"\t2113434\t2114327\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G7093-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C2567"\t"b2042"\t"b2042"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11857"\t"b3893"\t4081857\t4082759\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=FDOH-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C4843"\t"b3893"\t"b3893"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG12857"\t"b2586"\t2724128\t2724451\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG12857-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C3111"\t"b2586"\t"b2586"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG10421"\t"b2508"\t2632604\t2634070\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=IMP-DEHYDROG-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C3027"\t"b2508"\t"b2508"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=EG11066"\t"b4322"\t4551636\t4552820\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=MANNONDEHYDRAT-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C5402"\t"b4322"\t"b4322"\n+"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G6606"\t"b1166"\t1216369\t1216635\t"HTTPS://ecocyc.org/gene?orgid=ECOLI&id=G6606-MONOMER"\t"HTTPS://ecocyc.org/gene?orgid=ECOL199310&id=C1609"\t"b1166"\t"b1166"\n' 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| diff -r 785b6253af1f -r fe78fd6b315a rpviz/Test with Ecoli ntwk/E coli PPI network.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/Test with Ecoli ntwk/E coli PPI network.py Tue Jun 11 11:42:40 2019 -0400 |
| [ |
| @@ -0,0 +1,31 @@ +# -*- coding: utf-8 -*- +""" +Created on Tue May 28 11:38:34 2019 + +@author: Anaelle +""" + + +import networkx as nx +import numpy as np +import matplotlib.pyplot as plt +import requests + + +tab=np.loadtxt('HT.PMID-15690043.EcoliNet.303gene.3446link.txt',dtype='str',delimiter='\t') #Network file +smartab=np.loadtxt('Copy_of_All_genes_of_E._coli_K-12_substr._MG1655.txt', dtype='str',delimiter='\t',usecols=(0,1)) #Smart table to assign a link to each node + +reseau=nx.Graph() +dic_links={} +for i in range(len(tab)): + reseau.add_edge(tab[i][0],tab[i][1],weight=tab[i][2]) #network construction +for nodes in range(len(list(reseau.nodes))): + for j in range(len(smartab)): + if smartab[j][1][1:-1]==list(reseau.nodes)[nodes]: + url=smartab[j][0][1:-1] + left, right = url.split(':') + url_new = ':'.join( [left, requests.utils.quote(right)] ) #to avoid encoding problems + dic_links[list(reseau.nodes)[nodes]]= url_new#each link is assigned to each node + +nx.set_node_attributes(reseau,name='link',values=dic_links) +nx.write_gml(reseau,'reseau.gml') \ No newline at end of file |
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| diff -r 785b6253af1f -r fe78fd6b315a rpviz/Test with Ecoli ntwk/HT.PMID-15690043.EcoliNet.303gene.3446link.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/Test with Ecoli ntwk/HT.PMID-15690043.EcoliNet.303gene.3446link.txt Tue Jun 11 11:42:40 2019 -0400 |
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| b'@@ -0,0 +1,3446 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| diff -r 785b6253af1f -r fe78fd6b315a rpviz/csv_network.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/csv_network.py Tue Jun 11 11:42:40 2019 -0400 |
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| @@ -0,0 +1,60 @@ +# -*- coding: utf-8 -*- +""" +Created on Wed May 29 17:23:04 2019 + +@author: anael +Read the output of retropath +To visualize a csv file +""" + +import csv +import argparse +import os + +def arguments(): + parser = argparse.ArgumentParser(description='Visualizing a network from csv') + parser.add_argument('infile', + help='Input csv file.') + #parser.add_argument('outfile', + # help='Input some file.') + return parser + +parser = arguments() +arg = parser.parse_args() + +assert os.path.exists('infile/'+arg.infile) +file='infile/'+arg.infile +data=csv.reader(open(file)) +tab=[] +for ligne in data : + tab.append(ligne) + +List=[] #List of different number of pathways in the file +for i in range(1,len(tab)): + List.append(int(tab[i][0])) + List=list(set(List)) + List.sort() +for i in range(len(List)) : + nb=int(List[i]) + name=file+str(nb) + LR=[] + Lreact=[] + Lprod=[] + for i in range(len(tab)): + if tab[i][0]==str(nb) :#we chose the pathway + LR.append(tab[i][2]) #reaction = Unique ID + Lreact.append(tab[i][3].split(":")) + Lprod.append([tab[i][4]]) + #print('LR = '+ str(LR)) + #print('Lreact = '+ str(Lreact)) + #print('Lprod = '+ str(Lprod)) + #from nxvisualizer import network + #network(LR,Lreact,Lprod,name) + from network2json import network2 #to convert the lists in a json network + network2(LR,Lreact,Lprod,name) + + + + + + \ No newline at end of file |
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| diff -r 785b6253af1f -r fe78fd6b315a rpviz/main.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/main.py Tue Jun 11 11:42:40 2019 -0400 |
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| @@ -0,0 +1,56 @@ +# -*- coding: utf-8 -*- +""" +Created on Mon Jun 10 11:48:55 2019 + +@author: anael +""" + +import argparse +import os +from .sbml2lists import sbml2list +from .network2json import network2 +from .py2html2 import html2 + +def arguments(): + parser = argparse.ArgumentParser(description='Visualizing a network from sbml') + parser.add_argument('inputfolder', + help='Input folder with sbml files.') + parser.add_argument('outfile', + help='html file.') + return parser + +def run(infolder,outfile,test=True): + + if test: + folders=[infolder] + else: + folders=os.listdir(infolder) + json_elements={} + for f in folders: + if test: + file=f + else: + file=os.path.join(infolder,f) + output=sbml2list(file) + LR=output[0] + Lreact=output[1] + Lprod=output[2] + name=output[3] + species_smiles=output[4] + images=output[5] + species_names=output[6] + species_links=output[7] + + #from smile2picture import picture + #image=picture(species_smiles) + + + json_elements[name]=network2(LR,Lreact,Lprod,name,species_smiles,images,species_names,species_links) + + + html2(json_elements,outfile) + +if __name__ == '__main__': + parser = arguments() + arg = parser.parse_args() + run(arg.inputfolder,arg.outfile) |
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| diff -r 785b6253af1f -r fe78fd6b315a rpviz/network2json.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/network2json.py Tue Jun 11 11:42:40 2019 -0400 |
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| @@ -0,0 +1,61 @@ +# -*- coding: utf-8 -*- +""" +Created on Thu May 30 16:23:33 2019 + +@author: anael +""" + +import networkx as nx +import json + + + +def network2(LR,Lreact,Lprod,name,smile,image,spname,splinks): + ###Create the network with networkx + G=nx.DiGraph() + G.add_nodes_from(LR) #add reactions nodes + + + for i in range(len(LR)): + for j in range(len(Lreact[i])): + G.add_edge(Lreact[i][j],LR[i]) #add reactants nodes + for k in range(len(Lprod[i])): + G.add_edge(LR[i],Lprod[i][k]) #add products nodes + + #Attribute category + + dic_types={} + for i in range(len(LR)): + dic_types[(list(G.nodes))[i]]='reactions' + for node in range(len(list(G.nodes))): + if list(G.nodes)[node] in Lprod[i]: + dic_types[list(G.nodes)[node]]='product' + if list(G.nodes)[node] not in dic_types: + dic_types[list(G.nodes)[node]]='reactant' + nx.set_node_attributes(G,name='category',values=dic_types) + nx.draw(G) + + #Attribute smile + nx.set_node_attributes(G, name='smiles', values=smile) + + #Attribute image + nx.set_node_attributes(G,name='image', values=image) + + #Attribute name + nx.set_node_attributes(G,name='name', values=spname) + + #Attribute link + nx.set_node_attributes(G,name="link",values=splinks) + + js = nx.readwrite.json_graph.cytoscape_data(G) + json_elements=json.dumps(js) + + return(json_elements) + #file = os.path.join('file_json',name+'.json') + #json.dump(js,open(file,'w')) #doesn't work on Windows + + #from py2html import html + #html(file, name) + + #from py2html2 import html2 + #html2(file,name) \ No newline at end of file |
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| diff -r 785b6253af1f -r fe78fd6b315a rpviz/new_html/cytoscape.min.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/new_html/cytoscape.min.js Tue Jun 11 11:42:40 2019 -0400 |
| [ |
| b'@@ -0,0 +1,23 @@\n+/**\n+ * Copyright (c) 2016-2019, The Cytoscape Consortium.\n+ *\n+ * Permission is hereby granted, free of charge, to any person obtaining a copy of\n+ * this software and associated documentation files (the \xe2\x80\x9cSoftware\xe2\x80\x9d), to deal in\n+ * the Software without restriction, including without limitation the rights to\n+ * use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies\n+ * of the Software, and to permit persons to whom the Software is furnished to do\n+ * so, subject to the following conditions:\n+ *\n+ * The above copyright notice and this permission notice shall be included in all\n+ * copies or substantial portions of the Software.\n+ *\n+ * THE SOFTWARE IS PROVIDED \xe2\x80\x9cAS IS\xe2\x80\x9d, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\n+ * SOFTWARE.\n+ */\n+\n+!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?module.exports=t():"function"==typeof define&&define.amd?define(t):(e=e||self).cytoscape=t()}(this,function(){"use strict";function e(t){return(e="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(e){return typeof e}:function(e){return e&&"function"==typeof Symbol&&e.constructor===Symbol&&e!==Symbol.prototype?"symbol":typeof e})(t)}function t(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}function n(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}function r(e,t,r){return 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| b |
| diff -r 785b6253af1f -r fe78fd6b315a rpviz/new_html/output.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/new_html/output.html Tue Jun 11 11:42:40 2019 -0400 |
| [ |
| @@ -0,0 +1,112 @@ +<!DOCTYPE doctype html> +<html> + <head> + <meta charset="utf-8"/> + <title> + Viewer + </title> + <script id="elements"> + var rp_3={'nodes': [{'data': {'category': 'reactions', 'id': '<Reaction RP2>', 'value': '<Reaction RP2>', 'name': '<Reaction RP2>'}}, {'data': {'category': 'reactions', 'id': '<Reaction RP1>', 'value': '<Reaction RP1>', 'name': '<Reaction RP1>'}}, {'data': {'category': 'reactions', 'id': '<Reaction RP0>', 'value': '<Reaction RP0>', 'name': '<Reaction RP0>'}}, {'data': {'category': 'reactions', 'id': '<Reaction targetSink>', 'value': '<Reaction targetSink>', 'name': '<Reaction targetSink>'}}, {'data': {'category': 'reactant', 'name': '4-hydroxybenzoate', 'link': 'http://identifiers.org/metanetx.chemical/MNXM164', 'id': 'MNXM164__64__MNXC3', 'value': 'MNXM164__64__MNXC3'}}, {'data': {'category': 'reactant', 'name': 'H2O', 'link': 'http://identifiers.org/metanetx.chemical/MNXM2', 'id': 'MNXM2__64__MNXC3', 'value': 'MNXM2__64__MNXC3'}}, {'data': {'category': 'product', 'smiles': '[H]OC(=O)c1c([H])c([H])c([H])c([H])c1[H]', 'id': 'CMPD_0000000007__64__MNXC3', 'value': 'CMPD_0000000007__64__MNXC3', 'name': 'CMPD_0000000007__64__MNXC3'}}, {'data': {'category': 'reactant', 'name': 'NADH', 'link': 'http://identifiers.org/metanetx.chemical/MNXM10', 'id': 'MNXM10__64__MNXC3', 'value': 'MNXM10__64__MNXC3'}}, {'data': {'category': 'reactant', 'name': 'O2', 'link': 'http://identifiers.org/metanetx.chemical/MNXM4', 'id': 'MNXM4__64__MNXC3', 'value': 'MNXM4__64__MNXC3'}}, {'data': {'category': 'product', 'smiles': '[H]Oc1c([H])c([H])c([H])c([H])c1O[H]', 'id': 'CMPD_0000000003__64__MNXC3', 'value': 'CMPD_0000000003__64__MNXC3', 'name': 'CMPD_0000000003__64__MNXC3'}}, {'data': {'category': 'product', 'smiles': '[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]', 'id': 'TARGET_0000000001__64__MNXC3', 'value': 'TARGET_0000000001__64__MNXC3', 'name': 'TARGET_0000000001__64__MNXC3'}}], 'edges': [{'data': {'source': '<Reaction RP2>', 'target': 'CMPD_0000000007__64__MNXC3'}}, {'data': {'source': '<Reaction RP1>', 'target': 'CMPD_0000000003__64__MNXC3'}}, {'data': {'source': '<Reaction RP0>', 'target': 'TARGET_0000000001__64__MNXC3'}}, {'data': {'source': 'MNXM164__64__MNXC3', 'target': '<Reaction RP2>'}}, {'data': {'source': 'MNXM2__64__MNXC3', 'target': '<Reaction RP2>'}}, {'data': {'source': 'CMPD_0000000007__64__MNXC3', 'target': '<Reaction RP1>'}}, {'data': {'source': 'MNXM10__64__MNXC3', 'target': '<Reaction RP1>'}}, {'data': {'source': 'MNXM4__64__MNXC3', 'target': '<Reaction RP1>'}}, {'data': {'source': 'MNXM4__64__MNXC3', 'target': '<Reaction RP0>'}}, {'data': {'source': 'CMPD_0000000003__64__MNXC3', 'target': '<Reaction RP0>'}}, {'data': {'source': 'TARGET_0000000001__64__MNXC3', 'target': '<Reaction targetSink>'}}]} + var rp_7={'nodes': [{'data': {'category': 'reactions', 'id': '<Reaction RP2>', 'value': '<Reaction RP2>', 'name': '<Reaction RP2>'}}, {'data': {'category': 'reactions', 'id': '<Reaction RP1>', 'value': '<Reaction RP1>', 'name': '<Reaction RP1>'}}, {'data': {'category': 'reactions', 'id': '<Reaction RP0>', 'value': '<Reaction RP0>', 'name': '<Reaction RP0>'}}, {'data': {'category': 'reactions', 'id': '<Reaction targetSink>', 'value': '<Reaction targetSink>', 'name': '<Reaction targetSink>'}}, {'data': {'category': 'reactant', 'name': 'L-tyrosine', 'link': 'http://identifiers.org/metanetx.chemical/MNXM76', 'id': 'MNXM76__64__MNXC3', 'value': 'MNXM76__64__MNXC3'}}, {'data': {'category': 'product', 'smiles': '[H]Oc1c([H])c([H])c([H])c([H])c1[H]', 'id': 'CMPD_0000000009__64__MNXC3', 'value': 'CMPD_0000000009__64__MNXC3', 'name': 'CMPD_0000000009__64__MNXC3'}}, {'data': {'category': 'reactant', 'name': 'O2', 'link': 'http://identifiers.org/metanetx.chemical/MNXM4', 'id': 'MNXM4__64__MNXC3', 'value': 'MNXM4__64__MNXC3'}}, {'data': {'category': 'product', 'smiles': '[H]Oc1c([H])c([H])c([H])c([H])c1O[H]', 'id': 'CMPD_0000000003__64__MNXC3', 'value': 'CMPD_0000000003__64__MNXC3', 'name': 'CMPD_0000000003__64__MNXC3'}}, {'data': {'category': 'product', 'smiles': '[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]', 'id': 'TARGET_0000000001__64__MNXC3', 'value': 'TARGET_0000000001__64__MNXC3', 'name': 'TARGET_0000000001__64__MNXC3'}}], 'edges': [{'data': {'source': '<Reaction RP2>', 'target': 'CMPD_0000000009__64__MNXC3'}}, {'data': {'source': '<Reaction RP1>', 'target': 'CMPD_0000000003__64__MNXC3'}}, {'data': {'source': '<Reaction RP0>', 'target': 'TARGET_0000000001__64__MNXC3'}}, {'data': {'source': 'MNXM76__64__MNXC3', 'target': '<Reaction RP2>'}}, {'data': {'source': 'CMPD_0000000009__64__MNXC3', 'target': '<Reaction RP1>'}}, {'data': {'source': 'MNXM4__64__MNXC3', 'target': '<Reaction RP1>'}}, {'data': {'source': 'MNXM4__64__MNXC3', 'target': '<Reaction RP0>'}}, {'data': {'source': 'CMPD_0000000003__64__MNXC3', 'target': '<Reaction RP0>'}}, {'data': {'source': 'TARGET_0000000001__64__MNXC3', 'target': '<Reaction targetSink>'}}]} + </script> + <script id="svg"> + </script> + <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"> + </script> + <script src="cytoscape.min.js"> + </script> + <script> + function displaynet(network){ + var cy = cytoscape({ + container: $('#cy'), + + elements:network + , + + layout: { + name: 'breadthfirst', + //roots: "node[category = 'reactant']" + }, + + style: [ + { + selector: "node", + style: { + "background-color": '#80D0D0', + "label": "data(name)", + "font-size": "7px" + } + }, + {selector: "node[category='reactions']", + style: { + 'background-color': '#FA8072', + 'shape': 'roundrectangle' + }}, + {selector: "node[category='reactant']", + style: { + 'background-color': '#52be80', + }}, + { + selector: 'edge', + style: { + 'curve-style': 'bezier', + 'width': '3px', + 'target-arrow-shape': 'triangle', + } + }] + }); + + cy.on('mouseover','node',function(e){ + var node_select=e.target; + molecule=node_select.data("image"); + if(molecule){ + $("#molecule").attr('src',molecule); + $("#molecule").css( + {"width":"200px", + "height":"200px"});} + }); + cy.on('mouseout','node',function(e){ + $("#molecule").attr('src',""); + $("#molecule").css({ + "width":"", + "height":""}); + }); + + cy.on('tap','node',function(e){ + var node_select=e.target; + console.log(node_select.data("name")); + link=node_select.data("link"); + if(link){ + window.open(link) + }; + }); + }; + + $(function() { + }); + </script> + </head> + <style> + #cy { + width: 80%; + height: 100%; + position: absolute; + left : 20%; + } + + +#molecule{ + position : absolute; +} + </style> + <body> + <div id="cy"> + </div> + <img id="molecule" src=""/> + <form> + Choose a pathway : + <input onclick="displaynet(rp_3)" type="button" value="rp_3"/> + <input onclick="displaynet(rp_7)" type="button" value="rp_7"/> + </form> + </body> +</html> |
| b |
| diff -r 785b6253af1f -r fe78fd6b315a rpviz/new_html/template2.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/new_html/template2.html Tue Jun 11 11:42:40 2019 -0400 |
| [ |
| @@ -0,0 +1,106 @@ +<!doctype html> + +<html> + +<head> + <meta charset='utf-8'></meta> + <title>Viewer</title> + <script id="elements"></script> + <script id="svg"></script> + <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script> + <script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.0/cytoscape.min.js"></script> + <script> + function displaynet(network){ + var cy = cytoscape({ + container: $('#cy'), + + elements:network + , + + layout: { + name: 'breadthfirst', + //roots: "node[category = 'reactant']" + }, + + style: [ + { + selector: "node", + style: { + "background-color": '#80D0D0', + "label": "data(name)", + "font-size": "7px" + } + }, + {selector: "node[category='reactions']", + style: { + 'background-color': '#FA8072', + 'shape': 'roundrectangle' + }}, + {selector: "node[category='reactant']", + style: { + 'background-color': '#52be80', + }}, + { + selector: 'edge', + style: { + 'curve-style': 'bezier', + 'width': '3px', + 'target-arrow-shape': 'triangle', + } + }] + }); + + cy.on('mouseover','node',function(e){ + var node_select=e.target; + molecule=node_select.data("image"); + if(molecule){ + $("#molecule").attr('src',molecule); + $("#molecule").css( + {"width":"200px", + "height":"200px"});} + }); + cy.on('mouseout','node',function(e){ + $("#molecule").attr('src',""); + $("#molecule").css({ + "width":"", + "height":""}); + }); + + cy.on('tap','node',function(e){ + var node_select=e.target; + console.log(node_select.data("name")); + link=node_select.data("link"); + if(link){ + window.open(link) + }; + }); + }; + + $(function() { + }); + </script> +</head> + +<style> + #cy { + width: 80%; + height: 100%; + position: absolute; + left : 20%; + } + + +#molecule{ + position : absolute; +} + +</style> + +<body> + <div id="cy"></div> + <img id="molecule" src="" /> + <form> + Choose a pathway : + </form> +</body> +</html> |
| b |
| diff -r 785b6253af1f -r fe78fd6b315a rpviz/nxvisualizer.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/nxvisualizer.py Tue Jun 11 11:42:40 2019 -0400 |
| [ |
| @@ -0,0 +1,139 @@ +# -*- coding: utf-8 -*- +""" +Created on Thu May 30 10:21:48 2019 + +@author: anael +""" +#Usefull +import inspect +#inspect.getargspec(function) + +import networkx as nx +from IPython.display import Image +import requests +import json +import pandas as pd + +# Library for util +from py2cytoscape.data.cynetwork import CyNetwork +from py2cytoscape.data.cyrest_client import CyRestClient +from py2cytoscape.data.style import StyleUtil + + +def network(LR,Lreact,Lprod,name,smile,image): + ###Create the network with networkx + G=nx.DiGraph() + G.add_nodes_from(LR) #add reactions nodes + + + for i in range(len(LR)): + for j in range(len(Lreact[i])): + G.add_edge(Lreact[i][j],LR[i]) #add reactants nodes + for k in range(len(Lprod[i])): + G.add_edge(LR[i],Lprod[i][k]) #add products nodes + + #Attribute category + + dic_types={} + for i in range(len(LR)): + dic_types[(list(G.nodes))[i]]='reactions' + for node in range(len(list(G.nodes))): + if list(G.nodes)[node] in Lprod[i]: + dic_types[list(G.nodes)[node]]='product' + if list(G.nodes)[node] not in dic_types: + dic_types[list(G.nodes)[node]]='reactant' + print(dic_types) + nx.set_node_attributes(G,name='category',values=dic_types) + + #Attribute smile + nx.set_node_attributes(G, name='smiles', values=smile) + + #Attribute image + nx.set_node_attributes(G,name='image', values=image) + + nx.write_gml(G,name+'.gml') + + #Connect with cytoscape + cy = CyRestClient() + + # Reset + #cy.session.delete() + + #To create the network in cytoscape + network = cy.network.create_from_networkx(G, name=name, collection='My network collection') + print('New network created with py2cytoscape. Its SUID is ' + str(network.get_id())) + + #To get the SUID of all the components of the network + all_suid = cy.network.get_all() + net1 = cy.network.create(all_suid[0]) + print(net1.get_first_view()) + + #Styles + cy.layout.apply(name='hierarchical', network=network) + + # Get all existing Visual Styles + styles = cy.style.get_all() + print(json.dumps(styles, indent=4)) + + + # Get a reference to the existing style + default_style = cy.style.create('default') + print(default_style.get_name()) + + # Get all available Visual Properties + print(len(cy.style.vps.get_all())) + node_vps=cy.style.vps.get_node_visual_props() + edge_vps = cy.style.vps.get_edge_visual_props() + network_vps=cy.style.vps.get_network_visual_props() + print(pd.Series(edge_vps).head()) + print(pd.Series(node_vps).head()) + + + # Create a new style + style1 = cy.style.create("My_style") + print(style1.get_name()) + + + new_defaults = { + # Node defaults + 'NODE_FILL_COLOR': '#00ddee', + 'NODE_SIZE': 20, + 'NODE_BORDER_WIDTH': 0, + 'NODE_LABEL_COLOR': 'black', + + # Edge defaults + 'EDGE_WIDTH': 3, + 'EDGE_STROKE_UNSELECTED_PAINT': '#aaaaaa', + 'EDGE_LINE_TYPE': 'LONG_DASH', + 'EDGE_TARGET_ARROW_SHAPE' : 'DELTA', + + # Network defaults + 'NETWORK_BACKGROUND_PAINT': 'white', + } + + style1.update_defaults(new_defaults) + #Apply style + cy.style.apply(style1, network) + + # Passthrough mapping to get node labels + style1.create_passthrough_mapping(column='name', col_type='String', vp='NODE_LABEL') + + # Discrete mapping for node colours: + cat = { + 'reactant': '#4D833C', + 'product': '#C04E5D' + } + style1.create_discrete_mapping(column='category', + col_type='String', + vp='NODE_FILL_COLOR', + mappings=cat) + + # Discrete mapping for node shape: + reac = { + 'reactions': 'RECTANGLE' + } + style1.create_discrete_mapping(column='category', + col_type='String', + vp='NODE_SHAPE', + mappings=reac) + |
| b |
| diff -r 785b6253af1f -r fe78fd6b315a rpviz/py2html2.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/py2html2.py Tue Jun 11 11:42:40 2019 -0400 |
| [ |
| @@ -0,0 +1,45 @@ +# -*- coding: utf-8 -*- +""" +Created on Wed Jun 5 16:07:03 2019 + +@author: anael +""" + +import json +import os +from bs4 import BeautifulSoup + + +def html2(jsondata,outfile): + + htmlfile= open(os.path.join("new_html","template2.html")) + soup = BeautifulSoup(htmlfile, 'html.parser') + + for key in jsondata.keys(): + name=key + obj=json.loads(jsondata[key]) + elements=obj['elements'] + + element_script=soup.find(id="elements") #select the script section containing elements + element_script.append('\n var '+name+'='+str(elements)) #to modify + + form=soup.find('form') + new_tag = soup.new_tag("input") + new_tag["type"] = "button" + new_tag["value"]=name + new_tag["onclick"]="displaynet("+name+')' + form.append(new_tag) + try: + select=soup.find(id="selectbox") + new_tag=soup.new_tag("option") + new_tag["value"]=str(name) + new_tag.append(name) + select.append(new_tag) + except: + continue + + htmlfile.close() + + html = soup.prettify("utf-8") + with open(os.path.join(outfile), "wb") as file: + file.write(html) |
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| diff -r 785b6253af1f -r fe78fd6b315a rpviz/sbml2lists.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/sbml2lists.py Tue Jun 11 11:42:40 2019 -0400 |
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| @@ -0,0 +1,132 @@ +#!/usr/bin/env python +# coding: utf-8 +'''To visualize a SBML file''' +# In[3]: + + +import libsbml +import os +from .smile2picture import picture +#import networkx as nx +#import matplotlib.pyplot as plt + + + +# In[4]: +def sbml2list(file): + + #open the SBML using libsbml + + doc = libsbml.readSBML(file) + name=os.path.basename(file) + + + # In[8]: + + + #return the model from the SBML document using libsbml + model = doc.model + + + # In[9]: + + + #we will use the groups package to return the retropath pathway + #that is all the reactions that are associated with the heterologous + #pathway + groups = model.getPlugin('groups') + + + # In[10]: + + + #in the rpFBA script, rp_pathway is the default name + rp_pathway = groups.getGroup('rp_pathway') + + + # In[63]: + + rlist=[] + LR=[] + + heterologous_pathway_dG_prime_o = {} + + + #loop through all the members of the rp_pathway + for member in rp_pathway.getListOfMembers(): + #fetch the reaction according to the member id + reaction = model.getReaction(member.getIdRef()) + rlist.append(reaction) + LR.append(str(reaction)) + #get the annotation of the reaction + #includes the MIRIAM annotation and the IBISBA ones + annotation = reaction.getAnnotation() + ibisba_annotation = annotation.getChild('RDF').getChild('Ibisba').getChild('ibisba') + #extract one of the ibisba annotation values + heterologous_pathway_dG_prime_o[member.getIdRef()] = ibisba_annotation.getChild('dG_prime_o').getAttrValue('value') + + + + # In[64]: + + heterologous_pathway_dG_prime_o + + Lreact=[] + Lprod=[] + + for reaction in range(len(rlist)): + Lreact.append([p.species for p in rlist[reaction].reactants]) #get list of reactants id + Lprod.append([p.species for p in rlist[reaction].products]) #get list of products id + + mem = [] + for member in rp_pathway.getListOfMembers(): + reac = model.getReaction(member.getIdRef()) + for pro in reac.getListOfProducts(): + mem.append(pro.getSpecies()) + Lprod.append(pro.getSpecies()) + for rea in reac.getListOfReactants(): + mem.append(rea.getSpecies()) + Lreact.append(rea.getSpecies()) + + #mem = list(set([i for i in mem if i[0:3]!='MNX'])) + species_smiles = {} + species_links={} + species_names={} + #loop through all the members of the rp_pathway + for member in list(set([i for i in mem])): + #fetch the species according to the member id + reaction = model.getSpecies(member) + spname=reaction.getName() + if spname: + species_names[member]=spname + #get the annotation of the species + #includes the MIRIAM annotation and the IBISBA ones + annotation = reaction.getAnnotation() + ibisba_annotation = annotation.getChild('RDF').getChild('Ibisba').getChild('ibisba') + #extract one of the ibisba annotation values + smiles = ibisba_annotation.getChild('smiles').getChild(0).toXMLString() + if smiles: + species_smiles[member] = smiles + link_annotation=annotation.getChild('RDF').getChild('Description').getChild('is').getChild('Bag') + for i in range(link_annotation.getNumChildren()): + str_annot = link_annotation.getChild(i).getAttrValue(0) #Here we get the attribute at location "0". It works since there is only one + if str_annot.split('/')[-2]=='metanetx.chemical': + species_links[member]=str_annot #here is the MNX code returned + + + # In[64]: + + image=picture(species_smiles) + + return(LR, Lreact, Lprod, name, species_smiles,image, species_names, species_links) + + + + + #Cytoscape Network + #from nxvisualizer import network + #network(LR,Lreact,Lprod,name,species_smiles,image) + + #Convert network to json file + #from network2json import network2 #to convert the lists in a json network + #network2(LR,Lreact,Lprod,name,species_smiles,image,species_names,species_links) \ No newline at end of file |
| b |
| diff -r 785b6253af1f -r fe78fd6b315a rpviz/smile2picture.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz/smile2picture.py Tue Jun 11 11:42:40 2019 -0400 |
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| @@ -0,0 +1,26 @@ +# -*- coding: utf-8 -*- +""" +Created on Fri May 31 13:29:59 2019 + +@author: anael +""" + +from __future__ import print_function +from rdkit import Chem +from rdkit.Chem import rdDepictor +from rdkit.Chem.Draw import rdMolDraw2D + + +def picture(smile): + image={} + for i in smile : + mol = Chem.MolFromSmiles(smile[i]) + rdDepictor.Compute2DCoords(mol) + drawer = rdMolDraw2D.MolDraw2DSVG(200,200) + drawer.DrawMolecule(mol) + drawer.FinishDrawing() + svg = drawer.GetDrawingText() + image[i]=svg.split("?>\n")[1] + return(image) + + |
