def run(self):
global cnt
while True:
lock.acquire()
try:
d = target_file.next()
except:
lock.release()
break
sp = d.strip().split()
dirname = "down/%s" % sp[1]
try:
os.makedirs(dirname)
except:
pass
cnt += 1
if cnt % 10000 == 0:
print "downloading %d" % cnt
lock.release()
try:
wget.download(sp[2], out=dirname, bar=None)
except:
print("error downloading %s" % sp[2])
if(cnt >= 100): break
def DownloadData():
""" Downloads the shapefiles """
tar_dir = "./tars"
for dir in [shape_dir, tar_dir]:
if not os.path.exists(dir):
os.makedirs(dir)
base_url = "http://census.edina.ac.uk/ukborders/easy_download/prebuilt/shape/"
files_list = ["England_ct_2011_gen_clipped.tar.gz",
"England_ol_2011_gen_clipped.tar.gz",
"Wales_ct_1991_gen3.tar.gz",
"Wales_ol_2011_gen_clipped.tar.gz",
"Scotland_dt_1991.tar.gz",
"Scotland_ol_1991.tar.gz",
"Gb_dt_2009_10.tar.gz",
"Gb_wpc_2010_05.tar.gz"
]
print("Downloading shape files...")
for f in files_list:
if not os.path.exists(os.path.join(tar_dir, f)):
url = base_url + f
print("Downloading {}".format(url))
wget.download(url, out=tar_dir)
print()
print("Unpacking {}".format(f))
tar = tarfile.open(os.path.join(tar_dir, f))
tar.extractall(path=shape_dir)
tar.close()
print("Done, all shape-files stored in {}".format(shape_dir))
def load_sqlite(table, dbase, url=False, out=False):
"""
Retrieve triples from an sqlite3 database.
"""
if url:
# check for short path to url
if url.startswith('http://') or url.startswith('https://'):
pass
else:
url = 'http://tsv.lingpy.org/triples/'+url
print(url)
# check if file already exists
if os.path.isfile(dbase):
os.rename(
dbase,
dbase+'-backup-'+str(datetime.datetime.now()).split('.')[0]
)
wget.download(url, out=dbase)
db = sqlite3.connect(dbase)
cursor = db.cursor()
cursor.execute('select * from '+table+';')
data = cursor.fetchall()
return lingpy.basic.ops.triple2tsv(data, output='dict')
def __make_icon_osx():
lisa_shortcut = op.expanduser("~/Desktop/lisa")
if not os.path.exists(lisa_shortcut):
with open(lisa_shortcut, 'w') as outfile:
outfile.write(
"\
#!/bin/bash\n\
export PATH=$HOME/miniconda2/bin:$HOME/anaconda2/bin:$HOME/miniconda/bin:$HOME/anaconda/bin:$PATH\n\
lisa"
)
os.chmod(lisa_shortcut,
stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH |
stat.S_IRUSR | stat.S_IRGRP | stat.S_IXOTH |
stat.S_IWUSR | stat.S_IWGRP
)
import wget
lisa_icon_path= op.expanduser("~/lisa_data/.lisa/LISA256.icns")
if not os.path.exists(lisa_icon_path):
try:
wget.download(
"https://raw.githubusercontent.com/mjirik/lisa/master/applications/LISA256.icns",
out=lisa_icon_path
)
except:
logger.warning('logo download failed')
pass
def updateFiles(self):
print "Update Files"
# Clean out file array
self.data.params.files = []
# Always assume that the most up to date runtime is not yet available
runtime = ((self.current_time.hour-6) / 6) * 6 # Get the Model Runtime
if runtime < 0:
runtime = 0
launch_time_offset = self.launch_time - self.current_time
# For now, if the prediction take place in the past... don't
if launch_time_offset < timedelta(0):
launch_time_offset = timedelta(0)
prediction_offset = (launch_time_offset.seconds / 3600 / 3) * 3
### NOTE THIS ISN'T DONE!
self.data.params.files.append("./wind/49-43-290-294-%04d%02d%02d%02d-gfs.t%02dz.mastergrb2f%02d" % (self.current_time.year, self.current_time.month, self.current_time.day, prediction_offset, runtime, prediction_offset))
if not os.path.isfile("./wind/49-43-290-294-%04d%02d%02d%02d-gfs.t%02dz.mastergrb2f%02d" % (self.current_time.year, self.current_time.month, self.current_time.day, prediction_offset, runtime, prediction_offset)):
download_url = "http://nomads.ncep.noaa.gov/cgi-bin/filter_gfs_hd.pl?file=gfs.t%02dz.mastergrb2f%02d&leftlon=290&rightlon=294&toplat=49&bottomlat=43&dir=%%2Fgfs.%04d%02d%02d%02d%%2Fmaster" % (runtime, prediction_offset, self.launch_time.year, self.launch_time.month, self.launch_time.day, runtime)
print download_url
print (runtime, prediction_offset, self.current_time.year, self.current_time.month, self.current_time.day, runtime)
file = wget.download(download_url)
shutil.move(file, './wind/49-43-290-294-%04d%02d%02d%02d-%s' % (self.current_time.year, self.current_time.month, self.current_time.day, prediction_offset, file))
self.data.params.files.append("./wind/49-43-290-294-%04d%02d%02d%02d-gfs.t%02dz.mastergrb2f%02d" % (self.current_time.year, self.current_time.month, self.current_time.day, prediction_offset+3, runtime, prediction_offset+3))
if not os.path.isfile("./wind/49-43-290-294-%04d%02d%02d%02d-gfs.t%02dz.mastergrb2f%02d" % (self.current_time.year, self.current_time.month, self.current_time.day, prediction_offset+3, runtime, prediction_offset+3)):
download_url = "http://nomads.ncep.noaa.gov/cgi-bin/filter_gfs_hd.pl?file=gfs.t%02dz.mastergrb2f%02d&leftlon=290&rightlon=294&toplat=49&bottomlat=43&dir=%%2Fgfs.%04d%02d%02d%02d%%2Fmaster" % (runtime, prediction_offset+3, self.current_time.year, self.current_time.month, self.current_time.day, runtime)
file = wget.download(download_url)
shutil.move(file, './wind/49-43-290-294-%04d%02d%02d%02d-%s' % (self.current_time.year, self.current_time.month, self.current_time.day, prediction_offset+3, file))
def download_song(self, songTitle, song_ID, download_dir):
song_ID = str(song_ID)
download_url = (musicCrawler.music_download_url + song_ID + ".mp3")
song_local_path = os.path.join(download_dir, songTitle)
print(30 * "-")
print("Downloading Song: " + songTitle)
# handle exception if mp3 file is not found on url source
try:
wget.download(download_url, download_dir) # download the mp3 file from url to download directory
except Exception:
print("Song ", songTitle + " Not Found")
pass
# join the song Id with the download dir to get the song tittle path
song_ID = (song_ID+".mp3")
song_ID_path = os.path.join(download_dir, song_ID)
song_title_path = os.path.join(download_dir, songTitle)
try:
print("\n""Parsing Song: " + songTitle)
shutil.move(song_ID_path, song_title_path) # parse the song id with actual song name
print(30 * "-")
except FileNotFoundError:
print("Song ID ", song_ID + " Not Found")
pass
def download_file(filename, destination):
"""Download remote file using the `wget` Python module."""
destdir = os.path.split(destination)[0]
if not os.path.isdir(destdir):
os.makedirs(destdir)
url = get_remote_url(filename)
wget.download(url, out=destination)
def _download(self, url, checksum, dst):
import wget
retries = 0
while retries < 2:
if not os.path.exists(dst):
retries += 1
try:
wget.download(url, out=dst)
print
except Exception as e:
print
print 'error', e
continue
h = hashlib.sha1()
with open(dst, 'rb') as fp:
while True:
d = fp.read(4 * 1024 * 1024)
if not d:
break
h.update(d)
if h.hexdigest() == checksum:
break
print 'sha1 does not match: %s instead of %s' % (h.hexdigest(), checksum)
os.unlink(dst)
assert os.path.exists(dst), 'could not successfully retrieve %s' % url
def download_gif(self, term, slide_num):
# If we have at least 3 local gifs, use one of those
if (term in self.gifs) and (len(self.gifs[term]) > 3):
return os.path.join("GIFs", "%s.gif" % random.choice(self.gifs[term]))
try:
# Download the gif
#img = translate(term, app_key=self.GIPHY_API_KEY)
img = translate(term)
image_path = os.path.join(self.resources_dir, "%d.gif" % slide_num)
wget.download(img.media_url, image_path)
if not (term in self.gifs):
self.gifs[term] = []
if not (img.id in self.gifs[term]):
self.gifs[term].append(img.id)
shutil.copy(image_path, os.path.join("GIFs", "%s.gif" % img.id))
with open(os.path.join("GIFs", "hashes.json"), "w") as f:
json.dump(self.gifs, f, indent=2)
return image_path
except:
return None
def get_astrometry(self):
"""
Interact with astrometry.net to get the WCS for our image, using the
astrometry client code.
"""
# connect to astrometry.net
supernova_key = 'jhvrmcmwgufgmsrw'
supernova_url = 'http://supernova.astrometry.net/api/'
nova_key = 'tugzsuwnbcykkeuy'
nova_url = 'http://nova.astrometry.net/api/'
new_image = self.image.replace('.fits','.wcs.fits')
# The short routines below are pulled from astrometryClient/client.py in the __main__
c = anClient(apiurl=nova_url)
c.login(nova_key)
# upload the image
print '\n\nUploading image to astrometry.net\n\n'
kwargs = {'publicly_visible': 'y', 'allow_modifications': 'd', 'allow_commercial_use': 'd'}
upres = c.upload(self.image, **kwargs)
stat = upres['status']
if stat != 'success':
raise IOError('Upload failed: status %s\n %s\n' %(str(stat), str(upres)))
subID = upres['subid']
print '\n\nUpload successful. Submission id:',subID,'\n\n'
# Wait for the response
while True:
stat = c.sub_status(subID, justdict=True)
jobs = stat.get('jobs', [])
if len(jobs):
for j in jobs:
if j is not None:
break
if j is not None:
print '\n\nReceived job id',j,'\n\n'
jobID = j
break
time.sleep(5)
# wait for the calculation to finish
success = False
while True:
stat = c.job_status(jobID, justdict=True)
if stat.get('status','') in ['success']:
success = (stat['status'] == 'success')
break
time.sleep(5)
if not success:
raise IOError('astrometry.net query failed: status %s'%str(stat))
# download the new image
print '\n\nGrabbing solved image\n\n'
url = nova_url.replace('api','new_fits_file/%i' %jobID)
try:
os.remove( new_image )
except OSError:
pass
wget.download( url, out=new_image )
self.image = new_image
def main(argv=None):
if argv is None:
argv = sys.argv
print('Creating simple wiki serialized corpus')
# Download the raw file if we do not have it already
if not os.path.isfile(WIKIFILE):
# Get the file
wget.download(WIKIURL)
wiki = WikiCorpus(WIKIFILE, lemmatize=False)
i = 0
article_dict = {}
for text in wiki.get_texts(meta=True):
url_string = 'https://simple.wikipedia.org/wiki/?curid={}'
article_dict[i] = (url_string.format(text[0]), text[1])
i += 1
with open(ARTICLEDICT, 'w') as f:
json.dump(article_dict, f)
wiki.dictionary.filter_extremes(no_below=20, no_above=0.1,
keep_n=DEFAULT_DICT_SIZE)
MmCorpus.serialize(MMFILE, wiki, progress_cnt=10000, )
wiki.dictionary.save_as_text(DICTFILE)
print('Simple wiki serialized corpus created')
# Now run LSI
dictionary = Dictionary.load_from_text(DICTFILE)
mm = MmCorpus(MMFILE)
tfidf = TfidfModel(mm, id2word=dictionary, normalize=True)
tfidf.save(TDIFMODEL)
MmCorpus.serialize(TDIFFILE, tfidf[mm], progress_cnt=10000)
mm_tdif = MmCorpus(TDIFFILE)
lsi = LsiModel(mm_tdif, id2word=dictionary, num_topics=300)
index = similarities.MatrixSimilarity(lsi[mm_tdif])
index.save(SIMMATRIX)
lsi.save(LSIMODEL)
print("LSI model and index created")
def run(argv):
if not os.path.exists(clean_filepath):
print('dbsnp will be stored at {!r}'.format(clean_filepath))
if not os.path.exists(raw_filepath):
# dbSNP downloads are described at <https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/>
# This file includes chr-pos-ref-alt-rsid and 4X a bunch of useless columns:
dbsnp_url = 'ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b{}_GRCh37p13/VCF/00-All.vcf.gz'.format(dbsnp_version)
print('Downloading dbsnp!')
make_basedir(raw_filepath)
raw_tmp_filepath = get_tmp_path(raw_filepath)
wget.download(url=dbsnp_url, out=raw_tmp_filepath)
print('')
os.rename(raw_tmp_filepath, raw_filepath)
print('Done downloading.')
print('Converting {} -> {}'.format(raw_filepath, clean_filepath))
make_basedir(clean_filepath)
clean_tmp_filepath = get_tmp_path(clean_filepath)
run_script(r'''
gzip -cd '{raw_filepath}' |
grep -v '^#' |
perl -F'\t' -nale 'print "$F[0]\t$F[1]\t$F[2]\t$F[3]\t$F[4]"' | # Gotta declare that it's tab-delimited, else it's '\s+'-delimited I think.
gzip > '{clean_tmp_filepath}'
'''.format(raw_filepath=raw_filepath, clean_tmp_filepath=clean_tmp_filepath))
os.rename(clean_tmp_filepath, clean_filepath)
print("dbsnp is at '{clean_filepath}'".format(clean_filepath=clean_filepath))
def download_if_needed(url, filename):
""" Downloads the data from a given URL, if not already present in the directory, or displays any of the following:
1. The file already exists
2. URL does not exist
3. Server is not responding
"""
if os.path.exists(filename):
explanation = filename+ ' already exists'
return explanation
else:
try:
r = urlopen(url)
except URLError as e:
r = e
if r.code < 400:
wget.download(url)
explanation = 'downloading'
return explanation
elif r.code>=400 and r.code<500:
explanation = 'Url does not exist'
return explanation
else:
explanation = 'Server is not responding'
return explanation
def download_bigbird_models(): if not os.path.exists(RAW_DOWNLOAD_DIR): os.mkdir(RAW_DOWNLOAD_DIR) url = "http://rll.berkeley.edu/bigbird/aliases/772151f9ac/" req = urllib2.Request(url) res = urllib2.urlopen(req) html_split = res.read().split() model_names = [] for txt in html_split: if "/bigbird/images" in txt: model_names.append(txt[29:-5]) for model_name in model_names: print "" print model_name if not os.path.exists(RAW_DOWNLOAD_DIR + '/' + model_name): if os.path.exists(os.getcwd() + '/' + TAR_FILE_NAME): os.remove(os.getcwd() + '/' + TAR_FILE_NAME) download_url = "http://rll.berkeley.edu/bigbird/aliases/772151f9ac/export/" + model_name + "/" + TAR_FILE_NAME wget.download(download_url) t = tarfile.open(os.getcwd() + '/' + TAR_FILE_NAME, 'r') t.extractall(RAW_DOWNLOAD_DIR)
def _parse_page_urls_and_make_url_list(url_list, credentials, downloaddir, file_extns_of_intrest):
for url in url_list:
if credentials != None:
page_url = _convert_url_to_url_with_password(url, credentials)
else:
page_url = url
logger.info("downloading " + page_url)
try:
# remove any previously existing temp file, this is needed because if a file exists then
# wget does some name mangling to create a file with a different name and then that would
# need to be passed to BS4 and then ultimately that file would also be deleted, so just delete
# before hand.
if os.path.exists(TEMP_DOWNLOAD_FILE):
os.remove(TEMP_DOWNLOAD_FILE)
wget.download(page_url, TEMP_DOWNLOAD_FILE, bar=_download_progress_bar)
soup = BeautifulSoup(open(TEMP_DOWNLOAD_FILE))
links = soup.findAll(ANCHOR_TAG)
_make_list_of_download_candidates(page_url, links, downloaddir, file_extns_of_intrest)
except Exception, e:
logger.error("Exception: " + str(e))
def download_videos(m3u8_obj): print '[log] downloading videos' base_uri = m3u8_obj._base_uri for file in m3u8_obj.files: video_url = base_uri + "/" + file wget.download(video_url)
def gdb():
try:
gdb = dict()
pre1 = "http://sourceware.org/gdb/current/onlinedocs/"
pre2 = "https://sourceware.org/gdb/talks/esc-west-1999/"
gdb[1] = pre1 + "gdb.pdf.gz"
gdb[2] = pre2 + "paper.pdf"
gdb[3] = pre2 + "slides.pdf"
print stringa
print "GDB Documentation"
print "GDB User Manual"
filename = wget.download(gdb[1])
print "\nThe Heisenberg Debugging Technology"
print "Slides/Paper/Enter(for both)"
decision = raw_input()
if decision == "Paper":
filename = wget.download(gdb[2])
elif decision == "Slides":
filename = wget.download(gdb[3])
else:
for key in range(2,4):
# print key
filename = wget.download(gdb[key])
print "\nCompleted\n"
except:
print "\n Did something else happen ? \n"
def get_sdss_dr7_frame(run, camcol, field, band, rerun=40):
url, psfield_url, calib_url = \
get_sdss_dr7_frame_url(run, camcol, field, band, rerun)
# download files if necessary
import wget
if not os.path.exists(img_filename):
img_filename = wget.download(url)
if not os.path.exists(ps_filename):
ps_filename = wget.download(psfield_url)
# load calibration data to get sky noise
ps_data = fitsio.FITS(ps_filename)[6].read()
# create fitsfile
img_data = fitsio.FITS(img_filename)[0].read()
img_header = fitsio.read_header(img_filename)
import CelestePy.fits_image as fits_image
reload(fits_image)
imgfits = fits_image.FitsImage(band,
timg=imgs[band],
calib=1.,
gain=gain,
darkvar=darkvar,
sky=0.)
def download_gif(self, term, slide_num):
# If we have at least 3 local gifs, use one of those
if (term in self.gifs) and (len(self.gifs[term]) > 3):
return os.path.join("GIFs", "%s.gif" % random.choice(self.gifs[term]))
try:
# Download the gif
img = translate(term)
image_path = os.path.join(self.resources_dir, "%d.gif" % slide_num)
wget.download(img.fixed_height.url, image_path)
file_hasher = hashlib.md5()
with open(image_path, "rb") as f:
file_hasher.update(f.read())
file_md5 = file_hasher.hexdigest()
if not (term in self.gifs):
self.gifs[term] = []
if not (file_md5 in self.gifs[term]):
self.gifs[term].append(file_md5)
shutil.copy(image_path, os.path.join("GIFs", "%s.gif" % file_md5))
with open(os.path.join("GIFs", "hashes.json"), "w") as f:
json.dump(self.gifs, f, indent=2)
return image_path
except:
return None
def get_webapi_brand_image_link_per_country_lang(csku, lang=None, directory=None):
""" Accesses the Zalando Website API and pulls information for article brand, as well as a link
for an article picture.
:param csku: The csku name to pull data for
:param lang: The country to access
:type csku: str
:type lang: str-str
:return: The url of the csku picture, and the brand name of the csku
:rtype: dictionary_object
"""
try:
web_request = \
'https://api.zalando.com/articles/{c}?fields=media.images.largeHdUrl'.format(c=csku)
webapi_brand_image_url = requests.get(web_request, headers={'x-client-name': 'Team AIS Preorder PQRS API'})
result = json.loads(webapi_brand_image_url.text)
# In case of 404 http error or any http error.
# the result will be assigned here with the error message.
# Then the default values are returned.
if 'status' in result.keys():
raise DataNotFound
elif result is not None:
# Get the brand
if 'media' in result.keys() and 'images' in result['media'].keys():
for x in result['media']['images']:
if 'largeHdUrl' in x.keys():
pic_url = x['largeHdUrl']
wget.download(pic_url, out=directory)
except DataNotFound:
pass
def get_tles():
# GetTLEs(): returns a list of tuples of kepler parameters for each satellite.
resource = 'http://www.celestrak.com/norad/elements/resource.txt'
weather = 'http://www.celestrak.com/norad/elements/weather.txt'
try:
os.remove('resource.txt')
except OSError:
pass
try:
os.remove('weather.txt')
except OSError:
pass
wget.download(resource)
wget.download(weather)
file_names = ['weather.txt', 'resource.txt']
with open('tles.txt', 'w') as outfile:
for fname in file_names:
with open(fname) as infile:
for line in infile:
outfile.write(line)
tles = open('tles.txt', 'r').readlines()
print "retrieving TLE file.........."
# strip off the header tokens and newlines
tles = [item.strip() for item in tles]
# clean up the lines
tles = [(tles[i], tles[i+1], tles[i+2]) for i in xrange(0, len(tles)-2, 3)]
return tles
def _download(self):
if os.path.exists(self._target_file):
if self.overwrite:
log.info("Chose to overwrite old files.")
self._clean()
elif not self.verify():
log.error("Previous download seems corrupted.")
self._clean()
else:
log.info("Using previously downloaded %s" % self.filename)
return self.filename
elif not os.path.exists(self.directory):
log.debug("Creating %s" % self.directory)
os.mkdir(self.directory)
try:
for filename in [self.filename, self.filename + self.CHECKSUM_SUFFIX]:
log.debug("Downloading %s" % filename)
wget.download(self.base_url + filename, out=self.directory, bar=None)
if self.verify():
log.info(("Successfully downloaded: %s" % filename))
return self._target_file
else:
return None
except Exception as e:
log.debug("Failed to download %s: %s" % (filename, e))
def doTask(self, tstamp):
"""Download image."""
tstamp = coils.string2time(tstamp)
fname = coils.time2fname(tstamp) + '.jpg'
dest_dir = os.path.join(self._config['pics_dir'], coils.time2dir(tstamp))
dest_fname = os.path.join(
dest_dir,
fname,
)
if os.path.exists(dest_fname):
print('Skipping {}'.format(dest_fname))
return
try:
os.makedirs(dest_dir)
except os.error:
pass
saved = os.getcwd()
os.chdir(dest_dir)
url = '{}/pics/{}.jpg'.format(
self._url,
coils.time2fname(tstamp, full=True),
)
print(url)
wget.download(url, bar=None)
os.chdir(saved)
# Propagate timestamp downstream.
return tstamp
def foo():
fin=open(sys.argv[1],'r')
for line in fin:
a,b=line.strip().rstrip('\n').split(',')
c=b.strip('"')+'_'+a.strip('"')+'.pdf'
makeurl='http://www.tpcuiet.com/resume_upload/cannot_find_it_haha/{}'.format(c)
wget.download(makeurl)
def download(url):
"""Copy the contents of a file from a given URL
to a local file.
"""
wf = urllib2.urlopen(url)
html=wf.read()
# print html
flist=[]
mhdf = re.findall('\"M.*\.hdf\"', html)
mhdfs =[f for f in mhdf if 'h08v04' in f or 'h08v05' in f or 'h09v04' in f]
# print mhdfs
for line in mhdfs:
# print 'a line', line.replace('\"', '')
fileUrl=url+line.replace('\"', '')
print fileUrl
wget.download(fileUrl)
xhdf = re.findall('\"M.*\.hdf.xml\"', html)
xhdfs =[f for f in xhdf if 'h08v04' in f or 'h08v05' in f or 'h09v04' in f]
for line in xhdfs:
# print 'a line', line.replace('\"', '')
xfileUrl=url+line.replace('\"', '')
print xfileUrl
wget.download(xfileUrl)
def download_img(url):
text = requests.get(url).text
soup = bs(text, "lxml")
# total
total = soup.find('span', {'style': 'color: #DB0909'}).text
total = total[: -3]
total = int(total)
# title
title = soup.find('h1', {'id': 'htilte'}).text
url_pattern = soup.find('ul', {'id': 'hgallery'})
url_pattern = url_pattern.img.get('src').replace('/0.jpg', '/{:03d}.jpg')
print title
if os.path.exists(title):
return
os.mkdir(title)
for i in xrange(total):
file_url = url_pattern.format(i)
file_name = "{:03d}.jpg".format(i)
output_file = os.path.join(title, file_name)
if i == 0:
file_url = file_url.replace("000", "0")
wget.download(file_url, out=output_file)
def download_files(answer, download_list):
if answer == 'y' or answer == 'yes':
for item in download_list:
print item
wget.download(download_list[item])
else:
print 'Thank you and have a really great day!'
def update():
print("Downloading Update")
wget.download('<zip>', 'update.zip')
try:
shutil.rmtree(dir+'\config')
except:
print("Continuing")
try:
shutil.rmtree(dir+'\mods')
except:
print("Continuing")
try:
shutil.rmtree(dir+'\jarmods')
except:
print("Continuing")
with zipfile.ZipFile('update.zip') as myzip:
myzip.extractall(dir)
myzip.close()
os.remove('svn.txt')
os.remove('update.zip')
os.rename('svnnew.txt', 'svn.txt')
print("Update Complete")
def create_lisa_data_dir_tree(oseg=None):
odp = op.expanduser('~/lisa_data/.lisa/')
if not op.exists(odp):
os.makedirs(odp)
import wget
lisa_icon_path= path(".lisa/LISA256.png")
if not op.exists(lisa_icon_path):
try:
wget.download(
"https://raw.githubusercontent.com/mjirik/lisa/master/lisa/icons/LISA256.png",
out=lisa_icon_path)
except:
import traceback
logger.warning('logo download failed')
logger.warning(traceback.format_exc())
if oseg is not None:
# used for server sync
oseg._output_datapath_from_server = op.join(oseg.output_datapath, 'sync', oseg.sftp_username, "from_server/")
# used for server sync
oseg._output_datapath_to_server = op.join(oseg.output_datapath, 'sync', oseg.sftp_username, "to_server/")
odp = oseg.output_datapath
if not op.exists(odp):
os.makedirs(odp)
odp = oseg._output_datapath_from_server
if not op.exists(odp):
os.makedirs(odp)
odp = oseg._output_datapath_to_server
if not op.exists(odp):
os.makedirs(odp)
def get_ipr_hierarchy():
if not os.path.isfile('interpro.xml.gz'):
print 'downloading interpro data'
wget.download('ftp://ftp.ebi.ac.uk/pub/databases/interpro/Current/interpro.xml.gz')
#if os.path.isfile('interpro.hierarchy.p'):
# with open('interpro.hierarchy.p','rU') as filehandle:
# ipr_hierarchy = pickle.load(filehandle)
# return ipr_hierarchy
print 'preparing interpro data'
ipr_hierarchy = IprHierarchy()
with gzip.open('interpro.xml.gz','rb') as filehandle:
#filecontent = filehandle.read()
soup = BeautifulSoup(filehandle,'xml')
for domain in soup.find_all('interpro'):
name = str(domain.find('name').string)
parents_list = []
contains_list = []
child_list = []
found_in_list = []
domain_features = get_domain_features(domain)
ipr = IprObject(ID=domain['id'],name=name,domain_type=domain['type'],domain_features=domain_features)
ipr_hierarchy.update(ipr)
ipr_hierarchy.set_contained_by()
#print ipr_hierarchy
with open('interpro.hierarchy.p','w') as filehandle:
pickle.dump(ipr_hierarchy,filehandle)
return ipr_hierarchy
#!/usr/bin/env python3
# coding: utf-8
import os.path as osp
from collections import OrderedDict
import gdown
import torch
import tvm
import wget
from tvm import relay
wget.download('https://raw.githubusercontent.com/kosuke55/train_baiducnn/master/scripts/pytorch/BCNN.py') # noqa
from BCNN import BCNN
def fix_model_state_dict(state_dict):
new_state_dict = OrderedDict()
for k, v in state_dict.items():
name = k
if name.startswith('module.'):
name = name[7:] # remove 'module.' of dataparallel
new_state_dict[name] = v
return new_state_dict
current_dir = osp.dirname(osp.abspath(__file__))
data_dir = osp.join(current_dir, 'data')
pretrained_model = osp.join(data_dir, 'bestmodel.pt')
if not osp.exists(pretrained_model):
print('Downloading %s' % pretrained_model)
doc = open('/mnt/ddnfs/data_users/cxkttwl/ICL/BASS/err_stop_mzls.txt', 'w')
for kk in range(3):
if kk == 0:
lo = 180
else:
lo = 0
for jj in range(lo, len(z)):
ra_g = ra[jj]
dec_g = dec[jj]
z_g = z[jj]
try:
url_load = 'http://legacysurvey.org/viewer/fits-cutout?ra=%f&dec=%f&layer=dr8&pixscale=0.27&bands=%s&size=3000' % (
ra_g, dec_g, band[kk])
out_file = '/mnt/ddnfs/data_users/cxkttwl/ICL/BASS/mzls_img/mzls_img_ra%.3f_dec%.3f_z%.3f_%s_band.fits' % (
ra_g, dec_g, z_g, band[kk])
wt.download(url_load, out_file)
print('**********-----')
print('finish--', jj / len(z))
except:
s = '%s, %d, %.3f, %.3f, %.3f' % (band[kk], jj, ra_g, dec_g, z_g)
print(
s,
file=doc,
)
doc.close()
print('Done!')
async def ytmusic(client, message: Message):
global is_downloading
if is_downloading:
await message.reply_text("دانلود دیگری در جریان است بعدا تلاش کن")
return
urlissed = get_text(message)
pablo = await client.send_message(message.chat.id,
f"`{urlissed} در حال بارگیری`")
if not urlissed:
await pablo.edit("خطا")
return
search = SearchVideos(f"{urlissed}", offset=1, mode="dict", max_results=1)
mi = search.result()
mio = mi["search_result"]
mo = mio[0]["link"]
thum = mio[0]["title"]
fridayz = mio[0]["id"]
thums = mio[0]["channel"]
kekme = f"https://img.youtube.com/vi/{fridayz}/hqdefault.jpg"
await asyncio.sleep(0.6)
url = mo
sedlyf = wget.download(kekme)
opts = {
"format":
"best",
"addmetadata":
True,
"key":
"FFmpegMetadata",
"prefer_ffmpeg":
True,
"geo_bypass":
True,
"nocheckcertificate":
True,
"postprocessors": [{
"key": "FFmpegVideoConvertor",
"preferedformat": "mp4"
}],
"outtmpl":
"%(id)s.mp4",
"logtostderr":
False,
"quiet":
True,
}
try:
is_downloading = True
with youtube_dl.YoutubeDL(opts) as ytdl:
infoo = ytdl.extract_info(url, False)
duration = round(infoo["duration"] / 60)
if duration > 8:
await pablo.edit(
f" دقیقه است{duration}ویدیو های بیشتر از 8دقیقه دانلود نمیشوند. این مورد"
)
is_downloading = False
return
ytdl_data = ytdl.extract_info(url, download=True)
except Exception:
# await pablo.edit(event, f"**Failed To Download** \n**Error :** `{str(e)}`")
is_downloading = False
return
c_time = time.time()
file_stark = f"{ytdl_data['id']}.mp4"
capy = f"**عنوان ➠** `{thum}` **درخواست :** `{urlissed}` **چنل :** `{thums}` **لینک :** `{mo}`"
await client.send_video(
message.chat.id,
video=open(file_stark, "rb"),
duration=int(ytdl_data["duration"]),
file_name=str(ytdl_data["title"]),
thumb=sedlyf,
caption=capy,
supports_streaming=True,
progress=progress,
progress_args=(
pablo,
c_time,
f"`از یوتیوب {urlissed} در حال آپلود",
file_stark,
),
)
await pablo.delete()
is_downloading = False
for files in (sedlyf, file_stark):
if files and os.path.exists(files):
os.remove(files)
Path(download_path).mkdir(parents=True, exist_ok=True)
prophet_analysis_path = "/AURN_prophet_analysis"
Path(prophet_analysis_path).mkdir(parents=True, exist_ok=True)
meta_data_url = "https://uk-air.defra.gov.uk/openair/R_data/AURN_metadata.RData"
data_url = "https://uk-air.defra.gov.uk/openair/R_data/"
# Do you want to check the sites listed in the meta data file?
# Does the metadatafile exist?
meata_data_filename = 'AURN_metadata.RData'
if os.path.isfile(meata_data_filename) is True:
print("Meta data file already exists in this directory, will use this")
else:
print("Downloading Meta data file")
wget.download(meta_data_url)
# Read the RData file into a Pandas dataframe
metadata = pyreadr.read_r(meata_data_filename)
# In the following we now download the data. Here we have a number of options
# - Specify the years to download data for
# - Specify the local authority[ies] to download data for
# - Download data for all authorities
# Downloading site data for a specific year or years
years = [2015, 2016, 2017, 2018, 2019, 2020]
# If a single year is passed then convert to a list with a single value
if type(years) is int:
years = [years]
current_year = datetime.datetime.now()
pass
elif url[0] == "/":
url = baseURL + url
else:
url = baseURL + "/" + url
urllist.add(url)
for url in urllist:
filename = url.split("/")[-1]
if not os.path.isfile(filename.replace(" ", "%20")):
time.sleep(1)
if url[-3:] == "pdf":
response = requests.get(url)
if not response.status_code > 400:
url = url.replace(" ", "%20")
wget.download(url)
print("Downloading: " + url)
else:
print("404 for this guy: " + url)
elif url[-3:] == "html":
print(url)
response = requests.get(url)
if not response.status_code > 400:
url = url.replace(" ", "%20")
wget.download(url)
print("Downloading: " + url)
else:
print("404 for this guy: " + url)
elif url[-1] == "/":
p = re.compile("(crd\d{4})")
m = p.search(url)
async def ytmusic(client, message: Message):
global is_downloading
if is_downloading:
await message.reply_text(
"Another download is in progress, try again after sometime.")
return
urlissed = get_text(message)
pablo = await client.send_message(
message.chat.id,
f"`Getting {urlissed} From Youtube Servers. Please Wait.`")
if not urlissed:
await pablo.edit(
"Invalid Command Syntax, Please Check Help Menu To Know More!")
return
search = SearchVideos(f"{urlissed}", offset=1, mode="dict", max_results=1)
mi = search.result()
mio = mi["search_result"]
mo = mio[0]["link"]
thum = mio[0]["title"]
fridayz = mio[0]["id"]
thums = mio[0]["channel"]
kekme = f"https://img.youtube.com/vi/{fridayz}/hqdefault.jpg"
await asyncio.sleep(0.6)
url = mo
sedlyf = wget.download(kekme)
opts = {
"format":
"best",
"addmetadata":
True,
"key":
"FFmpegMetadata",
"prefer_ffmpeg":
True,
"geo_bypass":
True,
"nocheckcertificate":
True,
"postprocessors": [{
"key": "FFmpegVideoConvertor",
"preferedformat": "mp4"
}],
"outtmpl":
"%(id)s.mp4",
"logtostderr":
False,
"quiet":
True,
}
try:
is_downloading = True
with youtube_dl.YoutubeDL(opts) as ytdl:
infoo = ytdl.extract_info(url, False)
duration = round(infoo["duration"] / 60)
if duration > 8:
await pablo.edit(
f"❌ Videos longer than 8 minute(s) aren't allowed, the provided video is {duration} minute(s)"
)
is_downloading = False
return
ytdl_data = ytdl.extract_info(url, download=True)
except Exception as e:
#await pablo.edit(event, f"**Failed To Download** \n**Error :** `{str(e)}`")
is_downloading = False
return
c_time = time.time()
file_stark = f"{ytdl_data['id']}.mp4"
capy = f"**Video Name ➠** `{thum}` \n**Requested For :** `{urlissed}` \n**Channel :** `{thums}` \n**Link :** `{mo}`"
await client.send_video(
message.chat.id,
video=open(file_stark, "rb"),
duration=int(ytdl_data["duration"]),
file_name=str(ytdl_data["title"]),
thumb=sedlyf,
caption=capy,
supports_streaming=True,
progress=progress,
progress_args=(pablo, c_time,
f'`Uploading {urlissed} Song From YouTube Music!`',
file_stark))
await pablo.delete()
is_downloading = False
for files in (sedlyf, file_stark):
if files and os.path.exists(files):
os.remove(files)
import pandas as pd
import wget
from os import path
from time import strftime, sleep
# chk if file exist, if not download from LSE url
tmpfilename = 'tmp-' + str(strftime("%Y-%m")) + '-issues-IPOs.xlsx'
if path.exists('tmpdir/' + tmpfilename) == False:
## web UI = https://www.londonstockexchange.com/reports?tab=new-issues-and-ipos
# https://docs.londonstockexchange.com/sites/default/files/reports/New%20issues%20and%20IPOs_1.xlsx
url1 = 'https://docs.londonstockexchange.com/sites/default/files/reports/'
filexlsx = 'New issues and IPOs_1.xlsx'
wget.download(url1 + filexlsx, out='tmpdir/' + tmpfilename)
sleep(2)
dataexcel = pd.read_excel(
'tmpdir/' + tmpfilename,
sheet_name='New Issues and IPOs',
skiprows=range(6),
usecols=['Company', 'Date', 'Issue Price', 'Currency'])
comp_list = dataexcel['Company'].tolist()
date_list = dataexcel['Date'].tolist()
price_list = dataexcel['Issue Price'].fillna(0).tolist()
currc_list = dataexcel['Currency'].replace('GBX',
'GBP').fillna('PENCE').tolist()
company = [x for x in comp_list][::-1]
datejoin = [x.date() for x in date_list][::-1]
priceone = [x for x in price_list][::-1]
currency = [x for x in currc_list][::-1]
def __init__(self, config):
wget.download(
"https://dl.fbaipublicfiles.com/fasttext/supervised-models/lid.176.bin",
"model")
self.model = fasttext.load_model("model")
# получаем url и скачиваем картинку
p_url_img = b.select('.series__img-wrap')
string = p_url_img[0]
print(p_url_img)
ser_img = re.findall(fnd_src, str(p_url_img))
# Вынимаем название серии и дату
p_tit = b.select('.series__item .series__item-title')
p_dat = b.select('.series__month-day .series__item-month')
# получаем адрес серии
p_block = b.select('.series__link-block')
for ser in range(ser_num):
print(ser, ser_img[ser])
filename = wget.download(ser_img[ser])
os.rename(filename, u'' + os.getcwd() + '/' + filename)
ser_title = p_tit[ser].getText()
ser_dat = p_dat[ser].getText()
print('Серия: ' + str(ser) + ' ' + ser_title + ' дата:' + ser_dat)
result = re.findall(fnd_href, str(p_block[ser]))
# скачиваем
s1 = requests.get('http://www.tvc.ru' + result[0])
p = bs4.BeautifulSoup(s1.text, "html.parser")
# получаем анонс
p_anons = p.select('.brand__anons-text')
ser_anons = p_anons[0].getText()
print(
'Анонс: \n для ют. Православная энциклопедия ТВЦ \n для фб. #Православная_энциклопедия\n'
import argparse
import wget
# download dependencies
if not os.path.exists('data'):
DIRNAME = os.path.dirname(os.path.abspath(__file__))
DATA_DIR = os.path.join(DIRNAME, 'data')
os.mkdir(DATA_DIR)
ANNOTATIONS_TO_DOWNLOAD = [
('https://dl.fbaipublicfiles.com/qaoverlap/data/nq-annotations.jsonl','nq-annotations.jsonl'),
('https://dl.fbaipublicfiles.com/qaoverlap/data/triviaqa-annotations.jsonl', 'triviaqa-annotations.jsonl'),
('https://dl.fbaipublicfiles.com/qaoverlap/data/webquestions-annotations.jsonl','webquestions-annotations.jsonl')
]
for link, dest in ANNOTATIONS_TO_DOWNLOAD:
wget.download(link, os.path.join(DATA_DIR, dest))
ANNOTATIONS = [
'total',
'question_overlap',
'no_question_overlap',
'answer_overlap',
'no_answer_overlap',
'answer_overlap_only'
]
DIRNAME = os.path.dirname(os.path.abspath(__file__))
ANNOTATION_PATHS = {
'triviaqa': os.path.join(DIRNAME, 'data/triviaqa-annotations.jsonl'),
print('Его нельзя: ' + link)
elif link.find('youtube') != -1:
print('Его нельзя: ' + link)
elif link.find('text-lyrics.ru') != -1:
print('Яма: ' + link)
else:
print(link)
response = requests.get(link)
soup = BeautifulSoup(response.text,
'html.parser').find('div', class_='download')
print(soup)
if soup != None:
soup = soup.__str__()
for i in BeautifulSoup(soup, 'html.parser').find_all('a',
href=True):
wget.download(i['href'], 'Oxxymiron_where_test.mp3')
audio = MP3("Oxxymiron_where_test.mp3")
print("Track: " + audio.get("TIT2").text[0])
#try:print("Text: " + audio.get("USLT"))
#except AttributeError: print('Нет текста')
print('Lenght: ' + str(audio.info.length))
print('Info: ' + audio.info.pprint())
audio2 = MP3("Oxxymiron_where.mp3")
if audio2.get("TIT2") == audio.get(
"TIT2"
) and audio2.info.length == audio.info.length and audio2.info.pprint(
) == audio.info.pprint():
print("Это подлинный")
else:
def download(zip_path, path, to_download=True):
with ZipFile(wget.download(url, path), 'r') as zip_ref:
zip_ref.extractall(path)
# Where did you save your output from the Cross Validation fits?
#prophet_analysis_path = "/AURN_prophet_analysis"
prophet_analysis_path= 'C:/Users/Dave/Documents/Code/AURN_prophet_analysis'
#Path(prophet_analysis_path).mkdir(parents=True, exist_ok=True)
meta_data_url = "https://uk-air.defra.gov.uk/openair/R_data/AURN_metadata.RData"
data_url = "https://uk-air.defra.gov.uk/openair/R_data/"
# Do you want to check the sites listed in the meta data file?
# Does the metadatafile exist?
meata_data_filename = 'AURN_metadata.RData'
if os.path.isfile(meata_data_filename) is True:
print("Meta data file already exists in this directory, will use this")
else:
print("Downloading Meta data file")
wget.download(meta_data_url)
# Read the RData file into a Pandas dataframe
metadata = pyreadr.read_r(meata_data_filename)
# We do not download any AURN data in this script, since this will have taken
# place during the Prophet fitting process
# Nonetheless we can still choose to look at individual authorities
manual_selection = True
save_to_csv = False
site_data_dict=dict()
site_data_dict_name=dict()
diurnal_plot = True
if manual_selection is True:
def main(argv):
global logger, resultsFile, requiresAuth, user, pwd, queryListTxt, queries, runs, outliers, warmups, parallell, endpoint
configfile = False
config = False
# Read Config file
try:
opts, args = getopt.getopt(argv,"hc:",["config="])
except getopt.GetoptError:
print ('test.py -c <configfile>')
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print ('test.py -c <configfile>')
sys.exit()
elif opt in ("-c", "--config"):
configfile = arg
if not configfile:
print ('No config file given, usage:')
print ('test.py -c <configfile>')
sys.exit(2)
else:
print ('Config file is "', configfile)
config = yaml.safe_load(open(configfile))
if not config or config is None:
print ('Invalid config file given, try again or check the path to the config file, usage:')
print ('test.py -c <configfile>')
sys.exit(2)
else:
print ('Loaded config')
print (config)
##Set Benchmarker Parameters
#Log file
logger = logging.getLogger('Logger')
fhandler = logging.FileHandler(filename='output.log', mode='a')
formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
fhandler.setFormatter(formatter)
logger.addHandler(fhandler)
logger.setLevel(logging.DEBUG)
logger.propagate = False
#Store under test
store = config['storeUnderTest']
#Runner
url = "http://downloads.sourceforge.net/project/sparql-query-bm/2.1.0/sparql-query-bm-distribution.tar.gz"
fname = "sparql-query-bm-distribution.tar.gz"
dirname = "sparql-query-bm-2.1.0"
totalRuns = config['totalRuns'] #1 immediate, one after fixed time, one control run after same time interval
timeInterval = config['timeInterval'] #in seconds
checkDataLoaded = config['check_data_loaded']
#Target Endpoint
endpoint = config['endpoint']
sparqlEndpoint = SPARQLWrapper(endpoint)
requiresAuth = config['requiresAuth']
user = config['user']
pwd = config['pwd']
if requiresAuth:
sparqlEndpoint.setCredentials(user, pwd)
#Dataset
firstTriple = config['firstTriple']
lastTriple = config['lastTriple']
#Queries
queryListName = config['queryListName']
queryList = config['queryListSource'] + queryListName
queryListTxt = queryListName[:-3]+"txt"
queriesName = config['queriesName']
queries = config['queryListSource'] + queriesName + ".tar.gz"
#Benchmark
runs = config['runs']
outliers = config['outliers']
warmups = config['warmups']
parallell = config['parallell']
resultsFile = "results_"+store
#Install if necessary the Benchmarker Software
if not os.path.isfile(fname):
print ("Downloading: " + str(fname))
wget.download(url)
if not os.path.isdir(dirname):
print ("Untarring to dir: " + str(dirname))
untar(fname)
else:
print ("SPARQL Benchmarker already present in dir: " + str(dirname))
#Retrieve the queries
if not os.path.isfile(queryListName):
print ("Downloading: " +str(queryListName))
print("wget: " + str(queryList))
wget.download(queryList)
else:
print ("Query list already present: " + str(queryListName))
if not os.path.isfile(queryListTxt):
shutil.copyfile(queryListName, queryListTxt)
if not os.path.isfile(queriesName + ".tar.gz"):
print ("Downloading: " + str(queriesName))
wget.download(queries)
if not os.path.isdir(queriesName):
print ("Untarring to dir: " + str(queriesName))
extract(str(queriesName) + ".tar.gz")
else:
print ("Queries already present in dir: " + str(queriesName))
#Test if the endpoint is up and data is loaded and execute run
time.sleep(30)
if checkDataLoaded:
while ( not hasTriple(sparqlEndpoint, firstTriple) ) or (not hasTriple(sparqlEndpoint, lastTriple) ):
logger.info("This polls once a minute until data is loaded.")
time.sleep(60)
logger.info("All data is loaded.")
print("All data is loaded.")
logger.info("Running Queries")
print("Running Queries")
for x in range(0, totalRuns):
logger.info("Run %s of %s" % (x, totalRuns))
print("Run %s of %s" % (x, totalRuns))
rProc = run(x)
trace(rProc)
logger.info("Waiting %s for next run" % (timeInterval))
print("Waiting %s for next run" % (timeInterval))
time.sleep(timeInterval)
def get_nvd_feed():
url = 'https://nvd.nist.gov/feeds/json/cve/1.0/nvdcve-1.0-recent.json.zip' # NVD Feed URL
wget.download(url)
command = 'unzip -o nvdcve-1.0-recent.json.zip' # Unzip json.gz file
os.system(command)
imgplot.set_cmap('gray')
image = Image.fromarray(
tile_raster_images(X=W.numpy().T[10:11],
img_shape=(28, 28),
tile_shape=(1, 1),
tile_spacing=(1, 1)))
### Plot image
plt.rcParams['figure.figsize'] = (4.0, 4.0)
imgplot = plt.imshow(image)
imgplot.set_cmap('gray')
#>>>>>>>>>>>>>>>>>>Evaluation<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
if os.path.isfile('destructed3.jpg') is False:
url = 'https://ibm.box.com/shared/static/vvm1b63uvuxq88vbw9znpwu5ol380mco.jpg'
wget.download(url, 'destructed3.jpg')
img = Image.open('destructed3.jpg')
# convert the image to a 1d numpy array
sample_case = np.array(img.convert('I').resize((28, 28))).ravel().reshape(
(1, -1)) / 255.0
sample_case = tf.cast(sample_case, dtype=tf.float32)
hh0_p = tf.nn.sigmoid(tf.matmul(sample_case, W) + hb)
hh0_s = tf.round(hh0_p)
print("Probability nodes in hidden layer:", hh0_p)
print("activated nodes in hidden layer:", hh0_s)
# reconstruct
# Setup folders
print("Setting up install directories at /opt/caai")
if not os.path.exists('/opt/caai'):
Path('/opt/caai').mkdir(parents=True, exist_ok=True)
if not os.path.exists('/opt/caai/share'):
Path('/opt/caai/share').mkdir(parents=True, exist_ok=True)
if not os.path.exists('/opt/caai/bin'):
Path('/opt/caai/bin').mkdir(parents=True, exist_ok=True)
if not os.path.exists('/opt/caai/rhscripts'):
Path('/opt/caai/rhscripts').mkdir(parents=True, exist_ok=True)
# Download models
if not os.path.exists('models.zip'):
print('Downloading models for DeepMRAC')
url = "http://resolute.pet.rh.dk:8000/models_01sep2020.zip"
wget.download(url, 'models.zip')
print("")
# Unzip models
if not os.path.exists('/opt/caai/share/DeepMRAC'):
print("Extracting models")
with zipfile.ZipFile('models.zip', 'r') as zip_ref:
zip_ref.extractall('/opt/caai/share/DeepMRAC')
# Install scripts
print("Installing run scripts")
copyfile('scripts/process_DeepDixon_dicom.py',
'/opt/caai/bin/process_DeepDixon_dicom.py')
copymode('scripts/process_DeepDixon_dicom.py',
'/opt/caai/bin/process_DeepDixon_dicom.py')
# downloads the .bz2 file from the internet
import wget, os
if not os.path.isfile('first_actual_attempt/2015-12.bz2'):
wget.download('https://files.pushshift.io/reddit/comments/RC_2005-12.bz2',
'first_actual_attempt/2015-12.bz2')
import pandas as pd
import os
import wget
import zipfile
import glob
file = '/home/UA/jschroder/Downloads/ned_111.csv'
df = pd.read_csv(file,index_col=0)
DL_NED1 = '/workspace/Shared/Users/jschroder/TMP/DL_YQ'
if not os.path.exists(DL_NED1): os.makedirs(DL_NED1)
for i,k in zip(df.downloadURL , range(1,len(df.downloadURL)+1)) :
print 'downloading %s out of %s' %(k , len(df.downloadURL))
wget.download(i,out=DL_NED1)
for j in os.listdir(DL_NED1):
zfile = zipfile.ZipFile(os.path.join(DL_NED1,j))
zfile.extractall(DL_NED1)
a = DL_NED1
ls = [ os.path.join(a,i) for i in glob.glob(os.path.join(a,'*.img')) ]
tiles = ' '.join(map(str,ls))
full = os.path.join(a,'full.img')
full2 = os.path.join(a,'full3.img')
fulltiff =os.path.join(a,'full3.tif')
if __name__ == '__main__':
# 判断是否有新版本，没有新版本退出
ver_url = 'http://192.168.4.6/deploy/live_ver'
ver_fname = '/var/www/deploy/live_ver'
if not has_new_ver(ver_url, ver_fname):
print('未发现新版本。')
exit(1)
# 下载新版本文件
r = requests.get(ver_url)
ver_num = r.text.strip() # 去掉结尾的\n
down_dir = '/var/www/download'
app_url = 'http://192.168.4.6/deploy/pkgs/mysite-%s.tar.gz' % ver_num
wget.download(app_url, down_dir)
# 校验文件是否损坏，如果文件已损坏，则删除损坏文件并退出
app_fname = app_url.split('/')[-1]
app_fname = os.path.join(down_dir, app_fname)
md5_url = app_url + '.md5'
if not file_ok(app_fname, md5_url):
os.remove(app_fname)
print('文件已损坏')
exit(2)
# 部署新版本
deploy_dir = '/var/www/deploy'
dest = '/var/www/html/nsd1907'
deploy(app_fname, deploy_dir, dest)
#!/usr/bin/env python3
import wget
url = 'https://static.alta3.com/images/python/csv_users.txt'
wget.download(url, '/c/SDE-JS/Python/mycode/credmaker/csv_users.txt')
outFile = open("admin.rc", "a")
osAUTH = input("What is the OS_AUTH_URL?")
print("export OS_AUTH_URL=" + osAUTH, file=outFile)
print("export OS_IDENTITY_API_VERSION=3", file=outFile)
osPROJ = input("What is the OS_PROJECT_NAME?")
print("export OS_PROJECT_NAME=" + osPROJ, file=outFile)
osPROJDOM = input("What is the OS_PROJECT_DOMAIN_NAME?")
print("export OS_PROJECT_DOMAIN_NAME=" + osPROJDOM, file=outFile)
osUSER = input("What is the OS_USERNAME?")
print("export OS_USERNAME="******"What is the OS_USER_DOMAIN_NAME?")
print("export OS_USER_DOMAIN_NAME=" + osUSERDOM, file=outFile)
osPASS = input("What is the OS_PASSWORD?")
print("export OS_PASSWORD=" + osPASS, file=outFile)
outFile.close()
import requests
n = 2
for i in range(n):
API_URL = 'https://dog.ceo/api/breeds/image/random'
#API_KEY = 'i0cgsdYL3hpeOGkoGmA2TxzJ8LbbU1HpbkZo8B3kFG2bRKjx3V'
#headers = {'UserAPI-Key': API_KEY}
response = requests.get('{}'.format(API_URL))
data = response.json()
print(str(i) + " " + data['status'] + "-" + data['message'])
if (data['status'] == "success"):
fileurl = data['message']
urlsplit = fileurl.split('/')
breed = urlsplit[4]
fname = urlsplit[5]
newfilename = "images/" + breed + "---" + fname
# print(breed+"---"+fname)
# print(newfilename)
import wget
file_name = wget.download(fileurl)
import os
os.rename(fname, newfilename)
async def ytmusic(client, message: Message):
global is_downloading
if is_downloading:
await message.reply_text(
"Downloadan yang lain sedang berlangsung, coba lagi nanti")
return
urlissed = get_text(message)
pablo = await client.send_message(
message.chat.id,
f"`Mendapatkan {urlissed} Dari Youtube. Tunggu Sebentar.`")
if not urlissed:
await pablo.edit(
"Sintaks Perintah Tidak Valid, Silakan Periksa Menu Help Untuk Mengetahui Lebih Lanjut!"
)
return
search = SearchVideos(f"{urlissed}", offset=1, mode="dict", max_results=1)
mi = search.result()
mio = mi["search_result"]
mo = mio[0]["link"]
thum = mio[0]["title"]
fridayz = mio[0]["id"]
thums = mio[0]["channel"]
kekme = f"https://img.youtube.com/vi/{fridayz}/hqdefault.jpg"
await asyncio.sleep(0.6)
url = mo
sedlyf = wget.download(kekme)
opts = {
"format":
"best",
"addmetadata":
True,
"key":
"FFmpegMetadata",
"prefer_ffmpeg":
True,
"geo_bypass":
True,
"nocheckcertificate":
True,
"postprocessors": [{
"key": "FFmpegVideoConvertor",
"preferedformat": "mp4"
}],
"outtmpl":
"%(id)s.mp4",
"logtostderr":
False,
"quiet":
True,
}
try:
is_downloading = True
with youtube_dl.YoutubeDL(opts) as ytdl:
infoo = ytdl.extract_info(url, False)
duration = round(infoo["duration"] / 60)
if duration > 10:
await pablo.edit(
f"❌ Video berdurasi lebih dari 10 menit tidak diperbolehkan, video yang disediakan diperbolehkan {duration} minute(s)"
)
is_downloading = False
return
ytdl_data = ytdl.extract_info(url, download=True)
except Exception as e:
#await pablo.edit(event, f"**Failed To Download** \n**Error :** `{str(e)}`")
is_downloading = False
return
c_time = time.time()
file_stark = f"{ytdl_data['id']}.mp4"
capy = f"**Nama Video ➠** `{thum}` \n**Requested For :** `{urlissed}` \n**Channel :** `{thums}` \n**Link :** `{mo}`"
await client.send_video(
message.chat.id,
video=open(file_stark, "rb"),
duration=int(ytdl_data["duration"]),
file_name=str(ytdl_data["title"]),
thumb=sedlyf,
caption=capy,
supports_streaming=True,
progress=progress,
progress_args=(pablo, c_time,
f'`Uploading {urlissed} Song From YouTube Music!`',
file_stark))
await pablo.delete()
is_downloading = False
for files in (sedlyf, file_stark):
if files and os.path.exists(files):
os.remove(files)
async def mudapk(client, message):
pablo = await edit_or_reply(message, "`Searching For Mod App.....`")
sgname = get_text(message)
if not sgname:
await pablo.edit(
"`Please Give Me A Valid Input. You Can Check Help Menu To Know More!`"
)
return
PabloEscobar = (
f"https://an1.com/tags/MOD/?story={sgname}&do=search&subaction=search")
r = requests.get(PabloEscobar)
soup = BeautifulSoup(r.content, "html5lib")
mydivs = soup.find_all("div", {"class": "search-results"})
Pop = soup.find_all("div", {"class": "title"})
try:
sucker = mydivs[0]
except IndexError:
await pablo.edit("**404 Mod App Not Found!")
return
pH9 = sucker.find("a").contents[0]
file_name = pH9
pH = sucker.findAll("img")
imme = wget.download(pH[0]["src"])
Pablo = Pop[0].a["href"]
ro = requests.get(Pablo)
soup = BeautifulSoup(ro.content, "html5lib")
mydis = soup.find_all("a", {"class": "get-product"})
Lol = mydis[0]
lemk = "https://an1.com" + Lol["href"]
print(lemk)
rr = requests.get(lemk)
soup = BeautifulSoup(rr.content, "html5lib")
script = soup.find("script", type="text/javascript")
leek = re.search(r'href=[\'"]?([^\'" >]+)', script.text).group()
dl_link = leek[5:]
r = requests.get(dl_link)
await pablo.edit("Downloading Mod App")
ca = f"**App Name :** `{file_name}` \n\n**Uploaded Using @cpbotOT**"
open(f"{file_name}.apk", "wb").write(r.content)
c_time = time.time()
await pablo.edit(f"`Downloaded {file_name}! Now Uploading APK...`")
await client.send_document(
message.chat.id,
document=open(f"{file_name}.apk", "rb"),
thumb=imme,
caption=ca,
progress=progress,
progress_args=(
pablo,
c_time,
f"`Uploading {file_name} Mod App`",
f"{file_name}.apk",
),
)
os.remove(f"{file_name}.apk")
os.remove(imme)
await pablo.delete()
def phibase_mapping(base):
phi_base_blast_raw_df = pd.read_csv(
f"{base}/phibase/phibase_blast_raw.out", sep="\t", header=None)
phi_base_blast_mapping_df = pd.read_csv(
f"{base}/phibase/f_culmorum_phi_mapping.txt", sep="\t")
phi_base_blast_mapping_df.columns = ['Gene', 'Protein ID']
phi_fn = wget.download(
'https://raw.githubusercontent.com/PHI-base/data/master/releases/phi-base_current.csv',
out=f"{base}/phibase/")
phi_df = pd.read_csv(phi_fn, sep=",")
# Remove unamed columns
phi_df.drop(phi_df.columns[phi_df.columns.str.contains('unnamed',
case=False)],
axis=1,
inplace=True)
col_names = phi_df.columns
col_names_list = list(col_names)
phenotype_names = [x for x in col_names_list if 'phenotype' in x.lower()]
phi_series = phi_df['Pathogen species'].str.upper()
fusarium_index = phi_series[phi_series.str.contains(
"FUSARIUM")].index # 26 instances of Fusarium
fusarium_phi = phi_df[phi_df.index.isin(
fusarium_index)] # fusarium specific Phi results
updated_fusarium_df = fusarium_phi[[
'Gene', 'Gene ID', 'Protein ID', 'Host species', 'Pathogen species',
'Disease', 'Mutant Phenotype'
]]
updated_fusarium_df.reset_index(inplace=True)
del updated_fusarium_df['index']
disease_df = phibase_aggregate(updated_fusarium_df, 'Disease')
disease_df.to_csv(f"{base}/phibase/fusarium-phibase-disease.txt",
sep="\t",
index=None)
phenotype_df = phibase_aggregate(updated_fusarium_df, 'Mutant Phenotype')
phenotype_df.to_csv(f"{base}/phibase/fusarium-phibase-phenotype.txt",
sep="\t",
index=None)
gene_mapping_fusarium_phi_df = fusarium_phi[[
'Gene', 'Gene ID', 'Protein ID'
]]
gene_mapping_fusarium_phi_df.columns = [
'Gene name', 'Gene ID', 'Protein ID'
]
phi_base_blast_mapping_df = phi_base_blast_mapping_df.drop_duplicates(
subset='Gene', keep='first')
gene_name_phibase_merged = pd.merge(phi_base_blast_mapping_df,
gene_mapping_fusarium_phi_df,
on="Protein ID",
how='inner')
gene_name_phibase_merged = gene_name_phibase_merged[['Gene', 'Gene name']]
gene_name_phibase_merged = gene_name_phibase_merged.drop_duplicates(
subset='Gene name', keep='first')
updated_gene_names = []
for name in gene_name_phibase_merged['Gene name']:
if name.startswith("("):
updated_gene_names.append(name.replace("(", "").replace(")", ""))
elif "(" in name:
updated_gene_names.append(name.split('(', 1)[0])
else:
updated_gene_names.append(name)
gene_name_phibase_merged['Gene name'] = updated_gene_names
gene_name_phibase_merged['Gene'] = gene_name_phibase_merged[
'Gene'].str.replace("T", "G")
gene_name_phibase_merged.to_csv(
f"{base}/phibase/fusarium-phi-gene-mapping.txt", sep="\t", index=None)
phi_base_blast_raw_df = phi_base_blast_raw_df.drop_duplicates(subset=0,
keep='first')
phi_base_blast_raw_df.to_csv(f"{base}/phibase/phibase-blast-filtered.txt",
sep="\t",
index=None)
import os
os.getcwd()
import time
import selenium
from selenium import webdriver
from selenium.webdriver.common.by import By
driver = webdriver.Chrome(
executable_path='/home/jerry/Documents/Develop/chromedriver')
import wget
import urllib.request
url = 'https://www.google.com/search?q=%EB%90%9C%EC%9E%A5%EC%B0%8C%EA%B2%8C&tbm=isch&ved=2ahUKEwie1q_0xczsAhUG6ZQKHYlzDmQQ2-cCegQIABAA&oq=%EB%90%9C%EC%9E%A5%EC%B0%8C%EA%B2%8C&gs_lcp=CgNpbWcQAzICCAAyBggAEAoQGDIGCAAQChAYMgYIABAKEBgyBAgAEBgyBggAEAoQGDIGCAAQChAYMgYIABAKEBhQwaQcWJupHGC1rBxoAXAAeACAAcIBiAHKA5IBAzAuM5gBAKABAaoBC2d3cy13aXotaW1nwAEB&sclient=img&ei=PMKTX57ID4bS0wSJ57mgBg&bih=936&biw=916'
driver.get(url=url)
#elements=driver.find_elements(By.XPATH, '//img[@class="search-product-wrap-img"]')
elements = driver.find_elements(By.XPATH, '//img[@class="rg_i Q4LuWd"]')
down_path = '/home/jerry/Documents/Develop/pictures/'
for element in elements:
src = element.get_attribute('src')
#img_txt = src.split('/')[-1]
image_name = down_path #+img_txt
wget.download(url=src, out=image_name)
#islrg > div.islrc > div:nth-child(4) > a.wXeWr.islib.nfEiy.mM5pbd > div.bRMDJf.islir > img
# 한글 지원
# 잘되네 well done
print("Directory " + folderName + " already exists")
if not os.path.exists(fileFolderName):
os.mkdir(fileFolderName)
print("Directory " + fileFolderName + " Created ")
else:
print("Directory " + fileFolderName + " already exists")
i = 0
for doc_id in doc_id_list:
url_final = url_descarga_1 + doc_id + url_descarga_2
file_path = os.path.join(
fileFolderName, date_name + "&" + number_list[i] + "&" + entry_number_list[i])
print("\n" + file_path)
file_extension = utils.get_extension(url_final)
file_complete_path = file_path + "." + file_extension
if os.path.exists(file_complete_path):
os.remove(file_complete_path)
file_name = wget.download(url_final, file_complete_path)
if (file_extension != "pdf"):
utils.convert_to_pdf(file_name)
i = i + 1
input("\nPress any key to close")
print("MODEL_URL: " + MODEL_URL)
assert MODEL_URL is not None
# Get an unique ID
ID = str(uuid.uuid4())
# Create an empty dir
MODEL_FOLDER = join('models', ID)
if exists(MODEL_FOLDER):
shutil.rmtree(MODEL_FOLDER)
makedirs(MODEL_FOLDER)
print("MODEL_FOLDER: " + MODEL_FOLDER)
print("Downloading...")
filename = wget.download(MODEL_URL, MODEL_FOLDER)
print("FILENAME: " + filename)
print("OK")
print("Extracting...")
dataset_zip = zipfile.ZipFile(filename)
dataset_zip.extractall(MODEL_FOLDER)
dataset_zip.close()
remove(filename)
print("OK")
MODEL_PATH = None
LABELS_PATH = None
TEXT_PATH = None
for file in listdir(MODEL_FOLDER):
if file.endswith(".pt") or file.endswith(".pth") or file.endswith(".weights"):
input_manager.start()
QueueManager.register('get_output_queue', callable=lambda: output_queue)
output_manager = QueueManager(address=(HOST, OUTPUT_PORT), authkey=OUTPUT_AUTH)
output_manager.start()
model_file = 'efficientnet-edgetpu-M_quant_edgetpu.tflite'
model_name = 'efficientnet-edgetpu-M'
model_path = 'data/models/' + model_name + '/' + model_file
base_url = 'https://raw.githubusercontent.com/neuralet/neuralet-models/master/edge-tpu/'
url = base_url + model_name + '/' + model_file
if not os.path.isfile(model_path):
print('model does not exist, downloading from ', url)
wget.download(url, model_path)
def main():
interpreter = Interpreter(
model_path, experimental_delegates=[load_delegate("libedgetpu.so.1")])
interpreter.allocate_tensors()
input_details = interpreter.get_input_details()
output_details = interpreter.get_output_details()
input_queue = input_manager.get_input_queue()
output_queue = output_manager.get_output_queue()
print(
def retrieve_fasta_files():
# Fusarium oxysporum
fn_f_oxy_ensembl = wget.download(
'ftp://ftp.ensemblgenomes.org/pub/fungi/release-47/fasta/fusarium_oxysporum/pep/Fusarium_oxysporum.FO2.pep.all.fa.gz',
f'{base}/ensembl/fusarium_oxysporum.pep.fa.gz')
fn_f_oxy_ensembl = unzip_tidy(fn_f_oxy_ensembl, f'{base}/ensembl/')
# Read fasta file then filter it
with open(f'{fn_f_oxy_ensembl}', "r+") as handle:
SeqIO.write(yield_ensembl_records(fn_f_oxy_ensembl), handle, "fasta")
# A nidulans agdb
fn_f_nidulans_agdb = wget.download(
'http://www.aspergillusgenome.org/download/sequence/A_nidulans_FGSC_A4/current/A_nidulans_FGSC_A4_current_orf_coding.fasta.gz',
f'{base}/agdb/a_nidulans_orf.fa.gz')
fn_f_nidulans_agdb = unzip_tidy(fn_f_nidulans_agdb, '')
with open(f'{fn_f_nidulans_agdb}', "r+") as handle:
SeqIO.write(yield_ensembl_records(fn_f_nidulans_agdb), handle, "fasta")
# A nidulans Ensembl
fn_a_nid_ensembl = wget.download(
'ftp://ftp.ensemblgenomes.org/pub/fungi/release-47/fasta/aspergillus_nidulans/pep/Aspergillus_nidulans.ASM1142v1.pep.all.fa.gz',
f'{base}/ensembl/a_nidulans.pep.fa.gz')
fn_a_nid_ensembl = unzip_tidy(fn_a_nid_ensembl, '')
with open(f'{fn_a_nid_ensembl}', "r+") as handle:
SeqIO.write(yield_ensembl_records(fn_a_nid_ensembl), handle, "fasta")
# A nidulans UniProt
fn_a_nidulans_uniprot = wget.download(
'https://www.uniprot.org/uniprot/?query=reviewed:yes%20taxonomy:162425&format=fasta&force=true',
f'{base}/uniprot/a_nidulans_uniprot.fa')
with open(fn_a_nidulans_uniprot, "r+") as handle:
SeqIO.write(yield_records(fn_a_nidulans_uniprot, '|'), handle, "fasta")
# Fusarium graminearum
fn_gram_ensembl = wget.download(
'ftp://ftp.ensemblgenomes.org/pub/fungi/release-47/fasta/fusarium_graminearum/pep/Fusarium_graminearum.RR1.pep.all.fa.gz',
f'{base}/ensembl/fusarium_graminearum.pep.fa.gz')
fn_gram_ensembl = unzip_tidy(fn_gram_ensembl, f'{base}/ensembl/')
with open(f'{fn_gram_ensembl}', "r+") as handle:
SeqIO.write(yield_ensembl_records(fn_gram_ensembl), handle, "fasta")
# Fusarium gram UniProt
fn_gram_uniprot = wget.download(
'https://www.uniprot.org/uniprot/?query=reviewed:yes%20taxonomy:5506&format=fasta&force=true',
f'{base}/uniprot/fusarium_gram_uniprot.fa')
with open(fn_gram_uniprot, "r+") as handle:
SeqIO.write(yield_records(fn_gram_uniprot, '|'), handle, "fasta")
# Fusarium lang Ensembl
fn_lang_ensembl = wget.download(
'ftp://ftp.ensemblgenomes.org/pub/release-47/fungi/fasta/fungi_ascomycota3_collection/fusarium_langsethiae_gca_001292635/pep/Fusarium_langsethiae_gca_001292635.ASM129263v1.pep.all.fa.gz',
f'{base}/ensembl/fusarium_lang_uniprot.fa.gz')
fn_lang_ensembl = unzip_tidy(fn_lang_ensembl, f'')
with open(f'{fn_lang_ensembl}', "r+") as handle:
SeqIO.write(yield_ensembl_records(fn_lang_ensembl), handle, "fasta")
# Fusarium pesudo Ensembl
fn_psuedo_ensembl = wget.download(
'ftp://ftp.ensemblgenomes.org/pub/release-47/fungi/fasta/fusarium_pseudograminearum/pep/Fusarium_pseudograminearum.GCA_000303195.1.pep.all.fa.gz',
f'{base}/ensembl/fusarium_pseudogram.pep.fa.gz')
fn_psuedo_ensembl = unzip_tidy(fn_psuedo_ensembl, '')
with open(f'{fn_psuedo_ensembl}', "r+") as handle:
SeqIO.write(yield_ensembl_records(fn_psuedo_ensembl), handle, "fasta")
# Fusarium pesudo uniprot
fn_pesudo_uniprot = wget.download(
'https://www.uniprot.org/uniprot/?query=proteome:UP000007978&format=fasta&force=true',
f'{base}/uniprot/fusarium_pseudogram_uniprot.fa')
with open(fn_pesudo_uniprot, "r+") as handle:
SeqIO.write(yield_records(fn_pesudo_uniprot, '|'), handle, "fasta")
# Fusarium venenatum Ensembl
fn_venea_ensembl = wget.download(
'ftp://ftp.ensemblgenomes.org/pub/release-47/fungi/fasta/fungi_ascomycota4_collection/fusarium_venenatum_gca_900007375/pep/Fusarium_venenatum_gca_900007375.ASM90000737v1.pep.all.fa.gz',
f'{base}/ensembl/fusarim_venenatum.fa.gz')
fn_venea_ensembl = unzip_tidy(fn_venea_ensembl, '')
with open(f'{fn_venea_ensembl}', "r+") as handle:
SeqIO.write(yield_ensembl_records(fn_venea_ensembl), handle, "fasta")
# Fusarium evenen UniProt
fn_venea_uniprot = wget.download(
'https://www.uniprot.org/uniprot/?query=taxonomy:56646&format=fasta&force=true',
f'{base}/uniprot/fusarium_evenen_uniprot.fa')
with open(fn_venea_uniprot, "r+") as handle:
SeqIO.write(yield_records(fn_venea_uniprot, '|'), handle, "fasta")
# Magna Oryzae Ensembl
fn_magna_oryzae_ensembl = wget.download(
'ftp://ftp.ensemblgenomes.org/pub/release-47/fungi/fasta/magnaporthe_oryzae/pep/Magnaporthe_oryzae.MG8.pep.all.fa.gz',
f'{base}/ensembl/magna_oryzae_ensembl.pep.all.fa.gz')
fn_magna_oryzae_ensembl = unzip_tidy(fn_magna_oryzae_ensembl, '')
with open(f'{fn_magna_oryzae_ensembl}', "r+") as handle:
SeqIO.write(yield_ensembl_records(fn_magna_oryzae_ensembl), handle,
"fasta")
# Magna Oryzae UniProt
fn_magna_oryzae_uniprot = wget.download(
'https://www.uniprot.org/uniprot/?query=magnaporthe%20oryzae&format=fasta&force=true&sort=score&fil=reviewed:yes',
f'{base}/uniprot/magna_oryzae_uniprot.fa')
with open(fn_magna_oryzae_uniprot, "r+") as handle:
SeqIO.write(yield_records(fn_magna_oryzae_uniprot, '|'), handle,
"fasta")
# Ncrassa UniProt
fn_ncrassa_uniprot = wget.download(
'https://www.uniprot.org/uniprot/?query=neurospora%20crassa&format=fasta&force=true&sort=score&fil=reviewed:yes',
f'{base}/uniprot/ncrassa_uniprot.fa')
with open(fn_ncrassa_uniprot, "r+") as handle:
SeqIO.write(yield_records(fn_ncrassa_uniprot, '|'), handle, "fasta")
# Secrev UniProt
fn_s_cerevisiae_uniprot = wget.download(
'https://www.uniprot.org/uniprot/?query=saccharomyces%20cerevisiae&format=fasta&force=true&sort=score&fil=reviewed:yes',
f'{base}/uniprot/s_cerevisiae_uniprot.fa')
with open(fn_s_cerevisiae_uniprot, "r+") as handle:
SeqIO.write(yield_records(fn_s_cerevisiae_uniprot, '|'), handle,
"fasta")
# Secrev YGD
fn_s_cerevisiae_YGD = wget.download(
'http://sgd-archive.yeastgenome.org/sequence/S288C_reference/orf_protein/orf_trans.fasta.gz',
f'{base}/YGD/s_cerevisiae_YGD.fa.gz')
fn_s_cerevisiae_YGD = unzip_tidy(fn_s_cerevisiae_YGD, '')
ygd_id, hgnc = [], []
with open(fn_s_cerevisiae_YGD, "r+") as handle:
for v in handle:
if ">" in v:
ygd_id.append(v.split(" ")[0].replace(">", ""))
hgnc.append(v.split(" ")[1])
ygd_mapping_df = pd.DataFrame({'YGD ID': ygd_id, 'HGNC': hgnc})
ygd_mapping_df.to_csv(f'{base}/mapping/ygd_hgnc_mapping.txt',
sep="\t",
index=None)
with open(f'{fn_s_cerevisiae_YGD}', "r+") as handle:
SeqIO.write(yield_ensembl_records(fn_s_cerevisiae_YGD), handle,
"fasta")
# Zymo Ensembl
fn_z_trici = wget.download(
'ftp://ftp.ensemblgenomes.org/pub/release-47/fungi/fasta/zymoseptoria_tritici/pep/Zymoseptoria_tritici.MG2.pep.all.fa.gz',
f'{base}/ensembl/zymoseptoria_tritici.fa.gz')
fn_z_trici = unzip_tidy(fn_z_trici, '')
with open(f'{fn_z_trici}', "r+") as handle:
SeqIO.write(yield_ensembl_records(fn_z_trici), handle, "fasta")
# Zymo UniProt
fn_z_trici_uniprot = wget.download(
'https://www.uniprot.org/uniprot/?query=zymoseptoria&format=fasta&force=true&sort=score&fil=organism:%22Zymoseptoria%20tritici%20ST99CH_1A5%20[1276529]%22',
f'{base}/uniprot/zymoseptoria_tritici_uniprot.fa')
with open(fn_z_trici_uniprot, "r+") as handle:
SeqIO.write(yield_records(fn_z_trici_uniprot, '|'), handle, "fasta")
