def print_tree(self, tree, indent): for c in tree: if c in self.id_to_name: for i in range(indent): printf('\t') printf('%s\n', self.id_to_name[c]) self.print_tree(tree[c], indent + 1)
def print_tree(self, tree, indent): for c in tree: if c in self.id_to_name: for i in range(indent): printf('\t') printf('%s\n',self.id_to_name[c]) self.print_tree(tree[c], indent+1)
def construct_tree(self): self.tree['1'] = {} indent = 0 self.seen_tids = {} printf('%s\n',self.id_to_name['1']) self.seen_tids['1'] = 1 self.grow_tree(self.tree['1'],'1', indent+1) print "Leaf count " + str(self.leafcount)
def construct_tree(self): self.tree['1'] = {} indent = 0 self.seen_tids = {} printf('%s\n', self.id_to_name['1']) self.seen_tids['1'] = 1 self.grow_tree(self.tree['1'], '1', indent + 1) print "Leaf count " + str(self.leafcount)
def call_commands_serially(commands, status_update_callback, logger, stepslogger, params): """Run list of commands, one after another """ #logger.write("Executing commands.\n\n") from sys import exit make = False for c in commands: if c[3] == 'stop': print "Stopping!" return break if params['verbose']: eprintf("\n\n\nIssuing Command : %s\n", c[1]) eprintf("%s" % (c[0])) if c[3] in ['yes', 'redo'] and c[4]: result = getstatusoutput(c[1]) if result[0] == 0: if c[3] in ['redo']: eprintf('..... Redo Success!\n') else: eprintf('..... Success!\n') else: eprintf('..... Error!\n') #print c elif c[3] == 'grid' and c[4]: blastgrid(c[1]) continue elif c[3] == 'skip': eprintf('..... Skipping!\n') continue else: eprintf('..... Already Computed!\n') continue #status_update_callback('%s\n%s' %(result[0], result[0])) logger.write('COMMAND : \n%s \n' % (c[1])) if result[0] == 0: logger.write('Success!:\n%s\n' % (result[1])) else: #print result[1] try: printf('Error! : %s\n' % (result[1])) logger.write('Error!:\n%s\n' % (result[1])) except: pass break timestamp_pattern = '%Y-%m-%d %H:%M:%S' timestamp = datetime.now().strftime(timestamp_pattern) stepslogger.write('%s\t%s\n' % (c[2], timestamp))
def call_commands_serially(commands, status_update_callback, logger, stepslogger, params ): """Run list of commands, one after another """ #logger.write("Executing commands.\n\n") from sys import exit make = False for c in commands: if c[3]=='stop': print "Stopping!" return break if params['verbose']: eprintf("\n\n\nIssuing Command : %s\n", c[1]) eprintf("%s" %(c[0])) if c[3] in ['yes', 'redo' ] and c[4]: result = getstatusoutput(c[1]) if result[0] == 0 : if c[3] in ['redo']: eprintf('..... Redo Success!\n') else: eprintf('..... Success!\n') else: eprintf('..... Error!\n') #print c elif c[3]=='grid' and c[4]: blastgrid(c[1]) continue elif c[3]=='skip': eprintf('..... Skipping!\n') continue else: eprintf('..... Already Computed!\n') continue #status_update_callback('%s\n%s' %(result[0], result[0])) logger.write('COMMAND : \n%s \n' %( c[1])) if result[0] == 0 : logger.write('Success!:\n%s\n' %( result[1])) else: #print result[1] try: printf('Error! : %s\n' %(result[1])) logger.write('Error!:\n%s\n' %( result[1])) except: pass break timestamp_pattern='%Y-%m-%d %H:%M:%S' timestamp = datetime.now().strftime(timestamp_pattern) stepslogger.write('%s\t%s\n' %( c[2], timestamp))
def print_taxonomy_information(pathways,ranked_pathways, enzymes, enzymesmap): for key in ranked_pathways: taxons = {} for rxn in pathways[key]['rxns']: for enzyme in pathways[key]['rxns'][rxn]: taxons[pathways[key]['rxns'][rxn][enzyme]] = True #lca.build_independent_taxons(taxons) for rxn in pathways[key]['rxns']: print ' ' + rxn for enzyme in pathways[key]['rxns'][rxn]: printf("\t%s\t%s\n", enzyme, enzymesmap[pathways[key]['rxns'][rxn][enzyme]])
def print_taxonomy_information(pathways, ranked_pathways, enzymes, enzymesmap): for key in ranked_pathways: taxons = {} for rxn in pathways[key]['rxns']: for enzyme in pathways[key]['rxns'][rxn]: taxons[pathways[key]['rxns'][rxn][enzyme]] = True #lca.build_independent_taxons(taxons) for rxn in pathways[key]['rxns']: print ' ' + rxn for enzyme in pathways[key]['rxns'][rxn]: printf("\t%s\t%s\n", enzyme, enzymesmap[pathways[key]['rxns'][rxn][enzyme]])
def dry_run_status( commands ): for command in commands: printf("%s", command[0]) if command[4] == True: printf("%s", " Required") else: printf("%s", " Not Required") printf("\n")
def print_taxonomy_information(pathways, ranked_pathways, enzymes, lca): for key in ranked_pathways: print key taxons = [] for rxn in pathways[key]['rxns']: for enzyme in pathways[key]['rxns'][rxn]: taxons.append(pathways[key]['rxns'][rxn][enzyme]) lca.build_independent_taxons(taxons) for rxn in pathways[key]['rxns']: print ' ' + rxn for enzyme in pathways[key]['rxns'][rxn]: printf(" %s\t%s", enzyme, pathways[key]['rxns'][rxn][enzyme]) printf(" [ ") for child in lca.get_independent_parent( pathways[key]['rxns'][rxn][enzyme]): printf("\t%s", child) printf(" ]\n")
def call_commands_serially(commands, status_update_callback, logger, stepslogger, params ): """Run list of commands, one after another """ #logger.write("Executing commands.\n\n") from sys import exit make = False for c in commands: if c[3]=='stop': print "Stopping!" stepslogger.write('%s\t%s\n' %(c[2], "STOPPED")) return (0,'') if params['verbose']: eprintf("\n\n\nEXECUTED COMMAND : %s\n", c[1]) eprintf("%s" %(c[0])) stepslogger.write('%s\t%s\n' %(c[2], "RUNNING")) if c[3]=='missing': print "..... Input Missing!" stepslogger.write('%s\t%s\n' %(c[2], "INPUT_MISSING")) return (0,'') if c[3] in ['yes', 'redo' ] and c[4]: #result = getstatusoutput(c[1]) result = execute_pipeline_stage(c[1]) if result[0] == 0 : if c[3] in ['redo']: eprintf('..... Redo Success!\n') stepslogger.write('%s\t%s\n' %(c[2], "SUCCESS")) else: eprintf('..... Success!\n') stepslogger.write('%s\t%s\n' %(c[2], "SUCCESS")) else: eprintf('..... Failed!\n') stepslogger.write('%s\t%s\n' %(c[2], "FAILED")) #print c elif c[3]=='grid' and c[4]: blastgrid(c[1]) continue elif c[3]=='skip': eprintf('..... Skipping!\n') stepslogger.write('%s\t%s\n' %(c[2], "SKIPPED")) continue elif c[3]=='missing': eprintf('..... Input Missing!\n') stepslogger.write('%s\t%s\n' %(c[2], "INPUT_MISSING")) continue else: eprintf('..... Already Computed!\n') stepslogger.write('%s\t%s\n' %(c[2], "ALREADY_COMPUTED")) continue #status_update_callback('%s\n%s' %(result[0], result[0])) logger.write('COMMAND : \n%s \n' %( c[1])) if result[0] == 0 : logger.write('Success!:\n%s\n' %( result[1])) else: #print result[1] try: printf('Error! : %s\n' %(result[1])) logger.write('Error!:\n%s\n' %( result[1])) except: pass break