def test_KEGG_download(self): """ Download a KEGG pathway from the KEGG server and write KGML. """ # Download the KEGG ko01110 pathway, and render it pathway = retrieve_KEGG_pathway('ko01110') kgml_map = KGMLCanvas(pathway) kgml_map.import_imagemap = True kgml_map.draw(os.path.join('KEGG', 'ko01110.pdf')) # Download the KEGG ko01120 pathway and write to file as KGML retrieve_kgml_to_file("ko01120", os.path.join("KEGG", "ko01120.xml"))
koF.close() entryList = [e for e in keggPath.entries.values() if len(set(e.name.split()).intersection(koList))] return set(entryList) def colorMapItems(geneSet, color, width): for e in geneSet: for g in e.graphics: if g.type == 'line': g.fgcolor = color g.width = width g.bgcolor = color if not os.path.exists(args.outDir): os.makedirs(args.outDir) pathway = retrieve_KEGG_pathway(args.path) #pathway of interest #get KO numbers from previously created file #ko = ['ko:'+ ko for (trans,sp,ko) in (line.strip().split("\t") for line in (open(args.KO, 'r')))] knownKOSet = readKOFile(args.transKO, pathway) enhanceSet = knownKOSet if args.upKO != None: upKOSet = readKOFile(args.upKO, pathway) enhanceSet.update(upKOSet) if args.downKO != None: downKOSet = readKOFile(args.downKO, pathway) enhanceSet.update(downKOSet) notDE = set([e for e in pathway.orthologs if not len(set(e.name.split()).intersection(enhanceSet))])
############################ psr = argparse.ArgumentParser(description="Color KEGG maps with the Kegg Orthology entries that exist in your annotated transcriptome.") # kegg pathway name psr.add_argument('--path',help='Kegg Pathway Name', dest="path") # folder for map output psr.add_argument('--output',help='name of output folder', default = './', dest="outDir") # KO (for just presence/absence) psr.add_argument('--blastKO', help='Kegg Orthology from blast', dest='KO') ############################## args = psr.parse_args() ############################## if not os.path.exists(args.outDir): os.makedirs(args.outDir) pathway = retrieve_KEGG_pathway(args.path) #pathway of interest #pathway = read(args.path) #import pdb;pdb.set_trace() #get KO numbers from previously created file ko = ['ko:'+ ko for (trans,sp,ko) in (line.strip().split("\t") for line in (open(args.KO, 'r')))] #knownKOSet = set([e for e in pathway.entries.values() if len(set(e.name.split()).intersection(ko))]) knownKOSet = set([e for e in pathway.orthologs if len(set(e.name.split()).intersection(ko))]) def colorMapItems(geneSet, color, width): for e in geneSet: for g in e.graphics: if g.type == 'line': g.fgcolor = color g.width = width
import sys import os import urllib2 from KGML_scrape import retrieve_kgml_to_file, retrieve_KEGG_pathway from KGML_vis import KGMLCanvas goal_dir = os.path.dirname(os.path.abspath(__file__)) + "\..\Downloads" pathway = retrieve_KEGG_pathway(sys.argv[1]) kgml_map = KGMLCanvas(pathway) kgml_map.import_imagemap = True kgml_map.draw( os.path.join(os.path.normpath(goal_dir) + '\PDF', sys.argv[1] + '.pdf')) retrieve_kgml_to_file( sys.argv[1], os.path.join(os.path.normpath(goal_dir) + '\XML', sys.argv[1] + '.xml')) print sys.argv[1] + '.pdf'