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