def main(options, args):
logging.DEBUG = options('general.debug')
if len(args) != 3:
raise cli.MissingOptionError(
'Must specify PROJECT REPOPATH OUTPUTPATH, see --help')
project, repoPath, outputPath = args
if options('general.checkout') and options('general.export'):
raise cli.InvalidOptionError(
'You cannot specify both checkout and export')
logging.debugPrint(lambda: 'Loading repositories information...')
repositories = loadRepositories(options('general.config_dir'))
logging.debugPrint(lambda: 'Loaded repositories: %s' %
(' '.join(repositories.keys()), ))
if project not in repositories:
raise cli.InvalidOptionError('%s is not a valid project name' %
project)
repo = repositories[project]
branch = options('general.branch') or repo.branch
if not options('general.export') and (repo.exportType == CHECKOUT
or options('general.checkout')):
exportFunc = repo.rType.checkout
else:
exportFunc = repo.rType.export
exportFunc(options, repo, repoPath, outputPath, branch)
def blockOnTask(host, name, taskName, notifyF=logPrint, errorF=errorPrint):
endStates = [task.TASK_FAILED, task.TASK_COMPLETED]
state = None
prevTime = None
sleepTime = 1
time.sleep(sleepTime)
while state not in endStates:
tsk = loadTask(host, name, taskName)
state = tsk.state
if prevTime is None:
msgs = tsk.getMessages()
else:
msgs = tsk.getMessagesAfterTime(prevTime)
prevTime = tsk.timestamp
for m in msgs:
if m['mtype'] == task.MSG_ERROR:
errorF(m['text'])
elif m['mtype'] == task.MSG_NOTIFICATION:
notifyF(m['text'])
elif logging.DEBUG and m['mtype'] == task.MSG_SILENT:
debugPrint(lambda: m['text'])
##
# Make this configurable
if state not in endStates:
sleepTime = sleepTime < 30 and sleepTime * 2 or 30
time.sleep(sleepTime)
return state
def blockOnTask(host,
cluster,
taskName,
notifyF=logging.logPrint,
errorF=logging.errorPrint):
endStates = [task.TASK_FAILED, task.TASK_COMPLETED]
state = None
prevTime = None
sleepTime = 1
yield defer_utils.sleep(sleepTime)()
while state not in endStates:
tsk = yield tasks_client.loadTask(host, cluster, 'guest', taskName)
tsk = task.taskFromDict(tsk)
state = tsk.state
if prevTime is None:
msgs = tsk.getMessages()
else:
msgs = tsk.getMessagesAfterTime(prevTime)
prevTime = tsk.timestamp
for m in msgs:
if m['mtype'] == task.MSG_ERROR:
errorF(m['text'])
elif m['mtype'] == task.MSG_NOTIFICATION:
notifyF(m['text'])
elif logging.DEBUG and m['mtype'] == task.MSG_SILENT:
logging.debugPrint(lambda: m['text'])
##
# Make this configurable
if state not in endStates:
sleepTime = sleepTime < 30 and sleepTime * 2 or 30
yield defer_utils.sleep(sleepTime)()
defer.returnValue(state)
def monitorDownload(pr, downloaderChan, baseDir, url, minRate):
sizeSamples = []
while True:
baseSize = getSizeOfFiles(getDownloadFilenames(baseDir, url))
time.sleep(SAMPLE_RATE)
##
# If the program exited and exited correctly, then we're good
# otherwise take another sample size and see if we should terminate
if pr.exitCode is not None:
downloaderChan.receive()
return True
else:
currentSize = getSizeOfFiles(getDownloadFilenames(baseDir, url)) - baseSize
logging.debugPrint(lambda : 'Download rate: %8d - %s' % (currentSize/SAMPLE_RATE, getUrlFilename(url)))
size = currentSize/SAMPLE_RATE
if size < 0:
size = 0
sizeSamples.append(size)
if len(sizeSamples) > MAX_SAMPLE_SIZE:
sizeSamples.pop(0)
if len(sizeSamples) >= MAX_SAMPLE_SIZE and sum(sizeSamples)/len(sizeSamples) < minRate:
logging.logPrint('Average Rate: %8d - %s - KILLING' % (sum(sizeSamples)/len(sizeSamples), getUrlFilename(url)))
os.kill(pr.pipe.pid, signal.SIGTERM)
##
# Give it a second to finish up whatever it's doing
time.sleep(2)
try:
downloaderChan.receive()
except:
pass
return False
def monitorDownload(pr, downloaderChan, baseDir, url, minRate):
sizeSamples = []
while True:
baseSize = getSizeOfFiles(getDownloadFilenames(baseDir, url))
time.sleep(SAMPLE_RATE)
##
# If the program exited and exited correctly, then we're good
# otherwise take another sample size and see if we should terminate
if pr.exitCode is not None:
downloaderChan.receive()
return True
else:
currentSize = getSizeOfFiles(getDownloadFilenames(baseDir, url)) - baseSize
logging.debugPrint(lambda: "Download rate: %8d - %s" % (currentSize / SAMPLE_RATE, getUrlFilename(url)))
size = currentSize / SAMPLE_RATE
if size < 0:
size = 0
sizeSamples.append(size)
if len(sizeSamples) > MAX_SAMPLE_SIZE:
sizeSamples.pop(0)
if len(sizeSamples) >= MAX_SAMPLE_SIZE and sum(sizeSamples) / len(sizeSamples) < minRate:
logging.logPrint(
"Average Rate: %8d - %s - KILLING" % (sum(sizeSamples) / len(sizeSamples), getUrlFilename(url))
)
os.kill(pr.pipe.pid, signal.SIGTERM)
##
# Give it a second to finish up whatever it's doing
time.sleep(2)
try:
downloaderChan.receive()
except:
pass
return False
def blockOnTask(host, cluster, taskName, notifyF=logging.logPrint, errorF=logging.errorPrint):
endStates = [task.TASK_FAILED, task.TASK_COMPLETED]
state = None
prevTime = None
sleepTime = 1
yield defer_utils.sleep(sleepTime)()
while state not in endStates:
tsk = yield tasks_client.loadTask(host, cluster, 'guest', taskName)
tsk = task.taskFromDict(tsk)
state = tsk.state
if prevTime is None:
msgs = tsk.getMessages()
else:
msgs = tsk.getMessagesAfterTime(prevTime)
prevTime = tsk.timestamp
for m in msgs:
if m['mtype'] == task.MSG_ERROR:
errorF(m['text'])
elif m['mtype'] == task.MSG_NOTIFICATION:
notifyF(m['text'])
elif logging.DEBUG and m['mtype'] == task.MSG_SILENT:
logging.debugPrint(lambda : m['text'])
##
# Make this configurable
if state not in endStates:
sleepTime = sleepTime < 30 and sleepTime * 2 or 30
yield defer_utils.sleep(sleepTime)()
defer.returnValue(state)
def blockOnTask(host, name, taskName, notifyF=logPrint, errorF=errorPrint):
endStates = [task.TASK_FAILED, task.TASK_COMPLETED]
state = None
prevTime = None
sleepTime = 1
time.sleep(sleepTime)
while state not in endStates:
tsk = loadTask(host, name, taskName)
state = tsk.state
if prevTime is None:
msgs = tsk.getMessages()
else:
msgs = tsk.getMessagesAfterTime(prevTime)
prevTime = tsk.timestamp
for m in msgs:
if m['mtype'] == task.MSG_ERROR:
errorF(m['text'])
elif m['mtype'] == task.MSG_NOTIFICATION:
notifyF(m['text'])
elif logging.DEBUG and m['mtype'] == task.MSG_SILENT:
debugPrint(lambda : m['text'])
##
# Make this configurable
if state not in endStates:
sleepTime = sleepTime < 30 and sleepTime * 2 or 30
time.sleep(sleepTime)
return state
def main(options, args):
logging.DEBUG = options('general.debug')
if len(args) != 3:
raise cli.MissingOptionError('Must specify PROJECT REPOPATH OUTPUTPATH, see --help')
project, repoPath, outputPath = args
if options('general.checkout') and options('general.export'):
raise cli.InvalidOptionError('You cannot specify both checkout and export')
logging.debugPrint(lambda : 'Loading repositories information...')
repositories = loadRepositories(options('general.config_dir'))
logging.debugPrint(lambda : 'Loaded repositories: %s' % (' '.join(repositories.keys()),))
if project not in repositories:
raise cli.InvalidOptionError('%s is not a valid project name' % project)
repo = repositories[project]
branch = options('general.branch') or repo.branch
if not options('general.export') and (repo.exportType == CHECKOUT or options('general.checkout')):
exportFunc = repo.rType.checkout
else:
exportFunc = repo.rType.export
exportFunc(options, repo, repoPath, outputPath, branch)
def runDownloader(chan):
pr, rchan = chan.receive()
try:
commands.runProgramRunnerEx(pr)
logging.debugPrint(lambda: "Successfully completed download")
rchan.send(None)
except Exception, err:
logging.logPrint("Download failed for unknown reason: " + str(err))
rchan.sendError(err)
def runDownloader(chan):
pr, rchan = chan.receive()
try:
commands.runProgramRunnerEx(pr)
logging.debugPrint(lambda : 'Successfully completed download')
rchan.send(None)
except Exception, err:
logging.logPrint('Download failed for unknown reason: ' + str(err))
rchan.sendError(err)
def main(options, _args):
logging.DEBUG = options('general.debug')
cluster = cluster_ctl.loadCluster('local')
if cluster.ctype.NAME in ['EC2', 'Nimbus', 'DIAG']:
cluster = cluster.update(dataNodes=cluster.ctype.updateInstances(cluster.credInst, cluster.dataNodes),
execNodes=cluster.ctype.updateInstances(cluster.credInst, cluster.execNodes))
logging.debugPrint(lambda : 'Dumping new cluster')
cluster_ctl.saveCluster(cluster)
def STATE_IDLE(self, event):
self._log('In idle state, got message')
if event['event'] == 'start' and event['name'] == 'start pipeline:':
self.stateF = self.STATE_RUNNING
self.changed('state', self.state())
self._log('Got start message, switching to running state, starting update loop')
self.delayed = reactor.callLater(PIPELINE_UPDATE_FREQUENCY,
self.delayedLock.run,
self._waitForPipelineXmlRunningAndLoop)
else:
logging.debugPrint(lambda : repr(event))
def validMD5(options, url, md5):
if md5 is not None:
files = getDownloadFilenames(options("general.base_dir"), url)
if files:
files.sort()
newMd5 = calculateMD5(files)
logging.debugPrint(lambda: "Comparing %s to %s" % (md5, newMd5))
return md5 == newMd5
else:
False
else:
return True
def validMD5(options, url, md5):
if md5 is not None:
files = getDownloadFilenames(options('general.base_dir'), url)
if files:
files.sort()
newMd5 = calculateMD5(files)
logging.debugPrint(lambda : 'Comparing %s to %s' % (md5, newMd5))
return md5 == newMd5
else:
False
else:
return True
def STATE_IDLE(self, event):
self._log('In idle state, got message')
if event['event'] == 'start' and event['name'] == 'start pipeline:':
self.stateF = self.STATE_RUNNING
self.changed('state', self.state())
self._log(
'Got start message, switching to running state, starting update loop'
)
self.delayed = reactor.callLater(
PIPELINE_UPDATE_FREQUENCY, self.delayedLock.run,
self._waitForPipelineXmlRunningAndLoop)
else:
logging.debugPrint(lambda: repr(event))
def main(options, tasks):
if options('general.debug'):
logging.DEBUG = True
if not tasks:
debugPrint(lambda: 'No task names provided, loading all from database')
tasks = loadAllTasks(options('general.host'), options('general.name'))
else:
debugPrint(lambda: 'Task names provided, loading from database')
tasks = [
loadTask(options('general.host'), options('general.name'), t)
for t in tasks
]
if options('general.block'):
debugPrint(lambda: 'Blocking until tasks finish or fail')
tasks = blockOnTasks(options, tasks)
if options('general.no_completed'):
debugPrint(lambda: 'Removing any completed tasks')
tasks = filter(lambda t: t.state != task.TASK_COMPLETED, tasks)
##
# If there are tasks, find the largest, otherwise just return 0
maxTaskNameLen = tasks and max([len(t.name) for t in tasks]) or 0
printSpacing = False
for t in tasks:
if not printSpacing:
printSpacing = True
else:
print
print
printTask(options, t, maxTaskNameLen)
if options('general.exit_code'):
debugPrint(
lambda:
'Exiting with non-zero state if any tasks are not in a completed state'
)
notCompleted = [t for t in tasks if t.state != task.TASK_COMPLETED]
if notCompleted:
return 1
else:
return 0
return 0
def main(options, tasks):
if options('general.debug'):
logging.DEBUG = True
if not tasks:
debugPrint(lambda : 'No task names provided, loading all from database')
tasks = loadAllTasks(options('general.host'), options('general.name'))
else:
debugPrint(lambda : 'Task names provided, loading from database')
tasks = [loadTask(options('general.host'), options('general.name'), t)
for t in tasks]
if options('general.block'):
debugPrint(lambda : 'Blocking until tasks finish or fail')
tasks = blockOnTasks(options, tasks)
if options('general.no_completed'):
debugPrint(lambda : 'Removing any completed tasks')
tasks = filter(lambda t : t.state != task.TASK_COMPLETED, tasks)
##
# If there are tasks, find the largest, otherwise just return 0
maxTaskNameLen = tasks and max([len(t.name) for t in tasks]) or 0
printSpacing = False
for t in tasks:
if not printSpacing:
printSpacing = True
else:
print
print
printTask(options, t, maxTaskNameLen)
if options('general.exit_code'):
debugPrint(lambda : 'Exiting with non-zero state if any tasks are not in a completed state')
notCompleted = [t for t in tasks if t.state != task.TASK_COMPLETED]
if notCompleted:
return 1
else:
return 0
return 0
def attemptDownload(options, url):
cmd = ["wget", "-nv", "-P", options("general.base_dir")]
if options("general.continue_download"):
cmd.append("-c")
cmd.append(url)
pr = commands.ProgramRunner(" ".join(cmd), stdoutf=sys.stdout.write, stderrf=sys.stderr.write, log=True)
downloaderChan = threads.runThreadWithChannel(runDownloader).channel.sendWithChannel(pr)
##
# Wait 20 seconds or until files start appearing, if nothing appears
# then we will continue on to monitorDownload and it will fail out anyways
count = 20
while count > 0 and not getDownloadFilenames(options("general.base_dir"), url):
count -= 1
time.sleep(1)
logging.debugPrint(lambda: "Downloading with a minimum acceptable rate of %d" % options("general.min_rate"))
return monitorDownload(pr, downloaderChan, options("general.base_dir"), url, options("general.min_rate"))
def handleWWWObserver(request):
"""
Input:
{ id: string
file: string
event: string
retval: string
props: string
host: string
time: string
name: string
message: string
}
Output:
None
"""
logging.debugPrint(lambda: repr(request.body))
request.mq.send('/queue/pipelines/observer/' + request.body['props'],
json.dumps(request.body))
return defer_pipe.ret(request.update(response=None))
def handleWWWObserver(request):
"""
Input:
{ id: string
file: string
event: string
retval: string
props: string
host: string
time: string
name: string
message: string
}
Output:
None
"""
logging.debugPrint(lambda : repr(request.body))
request.mq.send('/queue/pipelines/observer/' + request.body['props'],
json.dumps(request.body))
return defer_pipe.ret(request.update(response=None))
def attemptDownload(options, url):
cmd = ['wget', '-nv', '-P', options('general.base_dir')]
if options('general.continue_download'):
cmd.append('-c')
cmd.append(url)
pr = commands.ProgramRunner(' '.join(cmd),
stdoutf=sys.stdout.write,
stderrf=sys.stderr.write,
log=True)
downloaderChan = threads.runThreadWithChannel(runDownloader).channel.sendWithChannel(pr)
##
# Wait 20 seconds or until files start appearing, if nothing appears
# then we will continue on to monitorDownload and it will fail out anyways
count = 20
while count > 0 and not getDownloadFilenames(options('general.base_dir'), url):
count -= 1
time.sleep(1)
logging.debugPrint(lambda : 'Downloading with a minimum acceptable rate of %d' % options('general.min_rate'))
return monitorDownload(pr, downloaderChan, options('general.base_dir'), url, options('general.min_rate'))
def update(self, who, aspect, value):
if aspect == 'load':
logging.debugPrint(lambda : 'TAG_NOTIFY: Sending LOAD ' + value.tagName)
self.mq.send(LOAD_TOPIC, json.dumps(value.tagName))
elif aspect == 'save':
logging.debugPrint(lambda : 'TAG_NOTIFY: Sending SAVE ' + value.tagName)
self.mq.send(SAVE_TOPIC, json.dumps(value.tagName))
elif aspect == 'remove':
logging.debugPrint(lambda : 'TAG_NOTIFY: Sending REMOVE ' + value)
self.mq.send(REMOVE_TOPIC, json.dumps(value))
def downloadUrls(chan):
(options, queue), rchan = chan.receive()
##
# Loop until queue is empty
try:
while True:
url, md5 = queue.get_nowait()
##
# Skip all this if it's already been downloaded
if md5 and validMD5(options, url, md5):
rchan.send((url, True))
continue
if not options('general.continue_download'):
logging.debugPrint(lambda : 'Deleting any files that already exist')
deleteDownloadedFiles(options('general.base_dir'), url)
time.sleep(1)
tries = options('general.tries')
try:
while (not attemptDownload(options, url) or not validMD5(options, url, md5)) and tries > 0:
logging.debugPrint(lambda : 'Download failed, trying again. %d' % tries)
if not options('general.continue_download'):
logging.debugPrint(lambda : 'Deleting downloaded files')
deleteDownloadedFiles(options('general.base_dir'), url)
time.sleep(1)
tries -= 1
if tries <= 0:
rchan.send((url, False))
else:
rchan.send((url, True))
except Exception, err:
logging.errorPrint('Download failed: ' + str(err))
rchan.send((url, False))
except Queue.Empty:
rchan.send(None)
def downloadUrls(chan):
(options, queue), rchan = chan.receive()
##
# Loop until queue is empty
try:
while True:
url, md5 = queue.get_nowait()
##
# Skip all this if it's already been downloaded
if md5 and validMD5(options, url, md5):
rchan.send((url, True))
continue
if not options("general.continue_download"):
logging.debugPrint(lambda: "Deleting any files that already exist")
deleteDownloadedFiles(options("general.base_dir"), url)
time.sleep(1)
tries = options("general.tries")
try:
while (not attemptDownload(options, url) or not validMD5(options, url, md5)) and tries > 0:
logging.debugPrint(lambda: "Download failed, trying again. %d" % tries)
if not options("general.continue_download"):
logging.debugPrint(lambda: "Deleting downloaded files")
deleteDownloadedFiles(options("general.base_dir"), url)
time.sleep(1)
tries -= 1
if tries <= 0:
rchan.send((url, False))
else:
rchan.send((url, True))
except Exception, err:
logging.errorPrint("Download failed: " + str(err))
rchan.send((url, False))
except Queue.Empty:
rchan.send(None)
def deleteDownloadedFiles(baseDir, url):
files = getDownloadFilenames(baseDir, url)
for f in files:
logging.debugPrint(lambda : 'Deleting: ' + f)
deleteFile(f)
def main(options, args):
logging.DEBUG = options('general.debug')
queue = Queue.Queue()
##
# Track the downloaded URL names for joining later if specified
urls = []
if not args:
for line in [l for l in sys.stdin if l.strip()]:
md5, url = line.split(' ', 1)
url = url.strip()
urls.append(url)
queue.put((url, md5))
else:
for url in args:
urls.append(url)
queue.put((url, None))
if options('general.join_name') and options('general.join_md5'):
md5 = calculateMD5([os.path.join(options('general.base_dir'), options('general.join_name'))])
##
# If they match, then no need to download and exit cleanly
if md5 == options('general.join_md5'):
return
retChans = [threads.runThreadWithChannel(downloadUrls).channel.sendWithChannel((options, queue)) for _ in range(options('general.max_threads'))]
successUrls = []
failedUrls = []
for c in retChans:
ret = c.receive()
while ret is not None:
url, succ = ret
if succ:
successUrls.append(url)
else:
failedUrls.append(url)
ret = c.receive()
if failedUrls:
for url in failedUrls:
logging.errorPrint(url)
##
# If any URLs failed, exit with fail
sys.exit(1)
else:
if options('general.join_name'):
logging.debugPrint(lambda : 'Joining files into: ' + options('general.join_name'))
files = []
for url in urls:
files.extend(sorted(getDownloadFilenames(options('general.base_dir'), url)))
fout = open(os.path.join(options('general.base_dir'), options('general.join_name')), 'wb')
for f in files:
logging.debugPrint(lambda : 'Reading: ' + f)
fin = open(f, 'rb')
d = fin.read(1000000)
while d:
fout.write(d)
d = fin.read(1000000)
fin.close()
fout.close()
logging.debugPrint(lambda : 'Deleting downloaded files after join')
for f in files:
logging.debugPrint(lambda : 'Deleting: ' + f)
deleteFile(f)
def main(options, args):
logging.DEBUG = options("general.debug")
queue = Queue.Queue()
##
# Track the downloaded URL names for joining later if specified
urls = []
if not args:
for line in [l for l in sys.stdin if l.strip()]:
md5, url = line.split(" ", 1)
url = url.strip()
urls.append(url)
queue.put((url, md5))
else:
for url in args:
urls.append(url)
queue.put((url, None))
if options("general.join_name") and options("general.join_md5"):
md5 = calculateMD5([os.path.join(options("general.base_dir"), options("general.join_name"))])
##
# If they match, then no need to download and exit cleanly
if md5 == options("general.join_md5"):
return
retChans = [
threads.runThreadWithChannel(downloadUrls).channel.sendWithChannel((options, queue))
for _ in range(options("general.max_threads"))
]
successUrls = []
failedUrls = []
for c in retChans:
ret = c.receive()
while ret is not None:
url, succ = ret
if succ:
successUrls.append(url)
else:
failedUrls.append(url)
ret = c.receive()
if failedUrls:
for url in failedUrls:
logging.errorPrint(url)
##
# If any URLs failed, exit with fail
sys.exit(1)
else:
if options("general.join_name"):
logging.debugPrint(lambda: "Joining files into: " + options("general.join_name"))
files = []
for url in urls:
files.extend(sorted(getDownloadFilenames(options("general.base_dir"), url)))
fout = open(os.path.join(options("general.base_dir"), options("general.join_name")), "wb")
for f in files:
logging.debugPrint(lambda: "Reading: " + f)
fin = open(f, "rb")
d = fin.read(1000000)
while d:
fout.write(d)
d = fin.read(1000000)
fin.close()
fout.close()
logging.debugPrint(lambda: "Deleting downloaded files after join")
for f in files:
logging.debugPrint(lambda: "Deleting: " + f)
deleteFile(f)
def deleteDownloadedFiles(baseDir, url):
files = getDownloadFilenames(baseDir, url)
for f in files:
logging.debugPrint(lambda: "Deleting: " + f)
deleteFile(f)
def _perform_workflow(data):
tn, f = data
outfile = open("%s.fasta" % tn, "w")
outfile.write(">%s\n%s" % (tn,f))
outfile.close()
logging.debugPrint(lambda : "Processing sequence: %s" % tn)
blast_against_reference("%s.fasta" % tn, combined, _temp_name(tn, "blast_parsed.txt"))
subprocess.check_call("sort -u -k 2,2 %s > %s" % (_temp_name(tn, "blast_parsed.txt"),
_temp_name(tn, "blast_unique.parsed.txt")),
shell=True)
parsed_blast_to_seqs(_temp_name(tn, "blast_unique.parsed.txt"), _temp_name(tn, "seqs_in.fas"))
check_and_align_seqs(_temp_name(tn, "seqs_in.fas"), num_refs, _temp_name(tn, "seqs_aligned.fas"))
if os.path.isfile(_temp_name(tn, "seqs_aligned.fas")):
"""What if there are NO SNPs in a given region"""
#try:
subprocess.call(['mothur',
'#filter.seqs(fasta=%s, soft=100, vertical=F)' % _temp_name(tn, "seqs_aligned.fas")], stdout=subprocess.PIPE)
subprocess.check_call('sed "s/[^1]/0/g" %s | sed "s/0/2/g" | sed "s/1/0/g" | sed "s/2/1/g" > %s' % (_temp_name(tn, "seqs_aligned.filter"),
_temp_name(tn, "mask.txt")), shell=True)
split_read(_temp_name(tn, "mask.txt"),_temp_name(tn, "padded.txt"))
sum_qual_reads(_temp_name(tn, "padded.txt"), _temp_name(tn,"polys.txt"))
#except:
# """This function was never created"""
# write_poly_zeros(_temp_name(tn, "padded.txt"), _temp_name(tn,"polys.txt"))
if "T" == run_r:
name = get_seq_name("%s.fasta" % tn)
subprocess.check_call("cat snps.r | R --slave --args %s %s.table %s.pdf 2> /dev/null" % (_temp_name(tn, "seqs_aligned.fas"), name, name),
shell=True)
os.system("mv %s.table ./R_output/%s.table.txt" % (name, name))
os.system("mv %s.pdf ./R_output/%s.plots.pdf" % (name, name))
else:
pass
subprocess.check_call("FastTree -nt -noboot %s > %s 2> /dev/null" % (_temp_name(tn, "seqs_aligned.fas"),
_temp_name(tn, "tmp.tree")),
shell=True)
run_dendropy("%s" % (_temp_name(tn, "tmp.tree")), tree, "%s" % (_temp_name(tn, "tmp.RF")))
run_dendropy_euclidian("%s" % (_temp_name(tn, "tmp.tree")), tree, "%s" % (_temp_name(tn, "tmp.EU")))
get_contig_length("%s.fasta" % tn, _temp_name(tn, "length.txt"))
thread_id = id(threading.current_thread())
thread_distance_file = str(thread_id) + '_distance.txt'
parse_rf_file(_temp_name(tn, "tmp.RF"), thread_distance_file)
thread_euclidian_file = str(thread_id) + "_euc_dist.txt"
parse_rf_file(_temp_name(tn, "tmp.EU"), thread_euclidian_file)
thread_name_file = str(thread_id) + '_name.txt'
write_strip_name("%s.fasta" % tn, thread_name_file)
polys_name_file = str(thread_id) + '_polys.txt'
parse_poly_file(_temp_name(tn, "polys.txt"), polys_name_file)
length_name_file = str(thread_id) + '_length.txt'
parse_poly_file(_temp_name(tn, "length.txt"), length_name_file)
try:
subprocess.check_call("rm mothur*", shell=True, stderr=open(os.devnull, 'w'))
except:
pass
subprocess.check_call(["rm",
_temp_name(tn, "blast_parsed.txt"),
"%s.fasta" % tn,
_temp_name(tn, "blast_unique.parsed.txt"),
_temp_name(tn, "seqs_in.fas"),
_temp_name(tn, "seqs_aligned.fas"),
_temp_name(tn, "tmp.tree"),
_temp_name(tn, "tmp.RF"),
_temp_name(tn, "tmp.EU"),
_temp_name(tn, "mask.txt"),
_temp_name(tn, "padded.txt"),
_temp_name(tn, "polys.txt"),
_temp_name(tn, "seqs_aligned.filter"),
_temp_name(tn, "length.txt"),
_temp_name(tn, "seqs_aligned.filter.fasta")])
return (thread_distance_file, thread_name_file, polys_name_file, length_name_file,
thread_euclidian_file)
else:
subprocess.check_call(["rm",
_temp_name(tn, "blast_parsed.txt"),
"%s.fasta" % tn,
_temp_name(tn, "blast_unique.parsed.txt"),
_temp_name(tn, "seqs_in.fas")])
