def rm(workflows,prompt_confirm,stage_number,all_stages_after):
"""
Deletes a workflow
"""
workflows = [ Workflow.objects.get(pk=w) if representsInt(w) else Workflow.objects.get(name=w)
for w in workflows.split(',') ]
for wf in workflows:
if stage_number:
stage = wf.stages.get(order_in_workflow=stage_number)
if not prompt_confirm or confirm('Are you sure you want to delete {0}{1}{2}?'.
format(wf,stage,' and all stages after it' if all_stages_after else ''),
default=False,timeout=60):
for s in wf.stages.filter(order_in_workflow__gt=stage.order_in_workflow-1) if all_stages_after else wf.stages.filter(order_in_workflow = stage.order_in_workflow):
s.delete()
else:
if not prompt_confirm or confirm('Are you sure you want to delete {0}?'.format(wf),default=False,timeout=60):
wf.delete()
def main(input_fastq, output_dir, chunksize, buffersize):
"""
Chunks a large fastq file into smaller pieces.
"""
chunk = 0
log.info('Opening {0}'.format(input_fastq))
if input_fastq.endswith('.gz'):
infile = gzip.open(input_fastq)
else:
infile = open(input_fastq, 'r')
output_prefix = os.path.basename(input_fastq)
output_prefix = re.search("(.+?)(_001)*\.(fastq|fq)(\.gz)*",
output_prefix).group(1)
#write chunks
while True:
chunk += 1
# generate output paths
new_filename = '{0}_{1:0>3}'.format(output_prefix, chunk)
output_path = os.path.join(output_dir, new_filename + '.fastq.gz')
if os.path.exists(output_path):
if not confirm(
'{0} already exists! Are you sure you want to overwrite the file?'
.format(output_path),
timeout=0):
return
log.info('Reading {0} lines and writing to: {1}'.format(
chunksize * 4, output_path))
#Read/Write
total_read = 0
outfile = gzip.open(output_path, 'wb')
while total_read < chunksize * 4:
data = list(islice(infile, buffersize * 4)) #read data
if len(data) == 0:
log.info('Done')
return
# Write what was read
outfile.writelines(data)
log.info('wrote {0} lines'.format(len(data)))
del (data)
total_read += buffersize * 4
outfile.close()
infile.close()
def main(input_fastq,output_dir,chunksize,buffersize):
"""
Chunks a large fastq file into smaller pieces.
"""
chunk = 0
log.info('Opening {0}'.format(input_fastq))
if input_fastq.endswith('.gz'):
infile = gzip.open(input_fastq)
else:
infile = open(input_fastq,'r')
output_prefix = os.path.basename(input_fastq)
output_prefix = re.search("(.+?)(_001)*\.(fastq|fq)(\.gz)*",output_prefix).group(1)
#write chunks
while True:
chunk += 1
# generate output paths
new_filename = '{0}_{1:0>3}'.format(output_prefix,chunk)
output_path = os.path.join(output_dir,new_filename+'.fastq.gz')
if os.path.exists(output_path):
if not confirm('{0} already exists! Are you sure you want to overwrite the file?'.format(output_path), timeout=0):
return
log.info('Reading {0} lines and writing to: {1}'.format(chunksize*4,output_path))
#Read/Write
total_read=0
outfile = gzip.open(output_path,'wb')
while total_read < chunksize*4:
data = list(islice(infile,buffersize*4)) #read data
if len(data) == 0:
log.info('Done')
return
# Write what was read
outfile.writelines(data)
log.info('wrote {0} lines'.format(len(data)))
del(data)
total_read += buffersize*4
outfile.close()
infile.close()
"""
Configuration
"""
from configobj import ConfigObj
import shutil
import os,sys
from cosmos.utils.helpers import confirm
user_home_path = os.path.expanduser('~')
cosmos_path = os.path.join(user_home_path,'.cosmos/')
config_path = os.path.join(cosmos_path,'config.ini')
cosmos_library_path = os.path.dirname(os.path.realpath(__file__))
default_config_path = os.path.join(cosmos_library_path,'default_config.ini')
if not os.path.exists(config_path):
if confirm('No configuration file exists, would you like to create a default one in {0}?'.format(config_path),default=True):
if not os.path.exists(os.path.dirname(config_path)):
os.mkdir(os.path.dirname(config_path))
shutil.copyfile(default_config_path,config_path)
print >> sys.stderr, "Done. Before proceeding, please edit {0}".format(default_config_path)
else:
sys.exit(1)
# Creating settings dictionary
co = ConfigObj(config_path)
settings = co.dict()
settings['cosmos_library_path'] = cosmos_library_path
settings['cosmos_path'] = cosmos_path
settings['config_path'] = config_path
settings['user_home_path'] = user_home_path
# Defaults
