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 execute_pipeline_stage(pipeline_command):
argv = [ x.strip() for x in pipeline_command.split() ]
funcname = re.sub(r'.py$','', argv[0])
funcname = re.sub(r'^.*/','', funcname)
args = argv[1:]
if hasattr(python_scripts, funcname):
methodtocall = getattr( getattr(python_scripts, funcname), funcname)
result = methodtocall(args)
else:
result = getstatusoutput(pipeline_command)
return result
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 format_db(formatdb_executable, seqType, refdb_sequence_file, algorithm):
if algorithm=='BLAST':
cmd='%s -dbtype %s -in %s' %(formatdb_executable, seqType, refdb_sequence_file)
if algorithm=='LAST':
dirname = os.path.dirname(refdb_sequence_file)
cmd='%s -p -c %s %s' %(formatdb_executable, refdb_sequence_file, refdb_sequence_file)
result= getstatusoutput(cmd)
if result[0]==0:
return True
else:
return False
def startPathwayTools(ptoolsExec):
cmd = ptoolsExec + " -api"
status = getstatusoutput(cmd)
