def __main__():
print "Quality and somatic filtering script starts at: %s\n" % datetime.datetime.now()
parser = argparse.ArgumentParser(description='Filter variants based on qulaity and somatic filters')
parser.add_argument('-i','--input_file', help='specify input file', required=True)
parser.add_argument('-f','--quality_somatic_filters', help='specify quality and somatic filters', required=True)
parser.add_argument('-p','--pairing', help='specify if sample paired with matched normal: paired or unpaired', required=True)
args = vars(parser.parse_args())
# variant_input_file = "bam_vcf_cnv_path.txt"
variant_summary = args['input_file']
filters = args['quality_somatic_filters']
pairing = args['pairing']
filtered_summary = ".".join([variant_summary, "filtered.tmp" ]).replace('.txt', '')
somatic_summary = ".".join([filtered_summary, "somatic.tmp"]).replace('.txt','')
filter_variants(variant_summary, filters, pairing, filtered_summary, somatic_summary)
# recalculate occurrence for filtered summary
out = make_occurrence_dict(filtered_summary)
gene_patients_occur = out[0]
var_patients_occur = out[1]
gene_variants_occur = out[2]
calculate_occurrence(filtered_summary, gene_patients_occur, var_patients_occur, gene_variants_occur)
# recalculate occurrence for somatic summary
if (os.path.isfile(somatic_summary)):
out = make_occurrence_dict(somatic_summary)
gene_patients_occur = out[0]
var_patients_occur = out[1]
gene_variants_occur = out[2]
calculate_occurrence(somatic_summary, gene_patients_occur, var_patients_occur, gene_variants_occur)
os.reomve(somatic_summary)
# remove intermediate files
os.remove(filtered_summary)
def __main__():
logger.info("Quality and somatic filtering script starts at: %s\n" %
datetime.datetime.now())
parser = argparse.ArgumentParser(
description='Filter variants based on qulaity and somatic filters')
parser.add_argument('-i',
'--input_file',
help='specify input file',
required=True)
parser.add_argument('-f',
'--quality_somatic_filters',
help='specify quality and somatic filters',
required=True)
parser.add_argument(
'-p',
'--pairing',
help='specify if sample paired with matched normal: paired or unpaired',
required=True)
args = vars(parser.parse_args())
logger.debug('some debug message')
logger.info('some info message')
logger.warning('some warning message')
logger.error('some error message')
logger.critical('some critical message')
# variant_input_file = "bam_vcf_cnv_path.txt"
variant_summary = args['input_file']
filters = args['quality_somatic_filters']
pairing = args['pairing']
filtered_summary = ".".join([variant_summary,
"filtered.tmp"]).replace('.txt', '')
somatic_summary = ".".join([filtered_summary,
"somatic.tmp"]).replace('.txt', '')
filter_variants(variant_summary, filters, pairing, filtered_summary,
somatic_summary)
# recalculate occurrence for filtered summary
out = make_occurrence_dict(filtered_summary)
gene_patients_occur = out[0]
var_patients_occur = out[1]
gene_variants_occur = out[2]
calculate_occurrence(filtered_summary, gene_patients_occur,
var_patients_occur, gene_variants_occur)
# recalculate occurrence for somatic summary
if (os.path.isfile(somatic_summary)):
out = make_occurrence_dict(somatic_summary)
gene_patients_occur = out[0]
var_patients_occur = out[1]
gene_variants_occur = out[2]
calculate_occurrence(somatic_summary, gene_patients_occur,
var_patients_occur, gene_variants_occur)
os.reomve(somatic_summary)
# remove intermediate files
os.remove(filtered_summary)
def scrape(url):
image_page = urllib.request.urlopen(url)
image_soup = BeautifulSoup(image_page)
for image_link in image_soup.findAll('a'):
# print(image_link.get('href'))
if "imgsrc" in image_link.get('href') and "jpg" in image_link.get('href'):
urllib.request.urlretrieve(image_link.get('href'), "local.jpg")
# TODO:mark all the sources in the image
# TODO:need a function to put this in the bolb and the DB
if random.randint(0,10) > 2:
#part of training set
link = upload_image(os.getcwd()+"/local.jpg", "comet_trainig")
print(link)
else:
# part of validation set
link = upload_image(os.getcwd()+"/local.jpg", "comet_validation")
print(link)
os.reomve("local.jpg")
break
def main():
"""\
Usage: sports-naarad [-h] [-F] [-C] live_score|news|[player_stats name] [-my_fav_team]
Get latest updates for football and cricket
Options:
-h, --help shows help(this) message
-F, --football [uefa,
barclay, fifa] Get football updates. The tournament for which you
want to get updates. One of the argumets from uefa,
barclay and fifa is compulsory.
-C, --cricket Get cricket updates for international matches.
[live-score, news,
,fixtures
player-stats[name]] Fields to get. `live-scores` to get live socre of
on-going matches, `news` to get latest news headlines,
`player-stats` to get statistics of player specified.
`fixtures` to get updates on upcoming matches.
Compulsory single argument. For football option you
can give additional options topscorer.
Use `-` instead of space in names.
--proxy To specify proxy. Defaults to system proxy. Take name of
a file. Sample -proxy http://username:password@host:port/
--unset-proxy Removes the proxy set by using --proxy option.
"""
useage = textwrap.dedent(main.__doc__)
args = sys.argv
if args[1] == '-h':
print(useage)
sys.exit(0)
try:
if '--proxy' in args:
with open(sys.path[0] + '/proxy.config', 'w') as f:
f.write(args[args.index('-proxy') + 1])
if '--unset-proxy' in args:
import os
os.reomve(sys.path[0] + '/proxy.config')
if args[1] == '-F' or args[1] == '--football' or args[1] == '-f':
if '-c' in args or '-C' in args or '--cricket' in args:
raise ValueError(
'Both Football and cricket cannot be specified')
if args[2] == 'uefa':
pass
elif args[2].lower() == 'barclay':
from sports_naarad.barclay import Barclay
if args[3].lower() == 'fixtures':
fixture = Barclay().Fixtures(type_return='dict')
header = ['Clubs', 'Time(UTC)', 'Location']
print(tabulate(fixture, headers=header,
tablefmt='fancy_grid', floatfmt=".2f"))
elif args[3].lower() == 'live-score':
print('\n'.join(Barclay().liveScore(type_return='dict')))
elif args[3].lower() == 'news':
news = Barclay().get_news_headlines(type_return='dict')
print()
for headline in news:
print('Headline: ' + headline + '\n' +
'link: ' + news[headline] + '\n')
elif args[3].lower() == 'player-stats':
stats = Barclay().playerStats(args[4], type_return='dict')
print()
for stat in stats:
print(stat + ': ' + stats[stat])
elif args[3].lower() == 'topscorer':
scorers = Barclay().topScorers(type_return='dict')
top_scorers = []
for names in scorers:
top_scorers.append((names, scorers[names]))
top_scorers = sorted(top_scorers, key=lambda x: int(x[1]))
top_scorers.reverse()
print(tabulate(top_scorers, headers=[
'Player Name', 'Goal Scored'], tablefmt='fancy_grid'))
else:
raise ValueError(
'Not a Valid argument!\n Use -h option for help.')
elif args[2] == 'fifa':
pass
else:
raise ValueError(
'Not a Valid argument!\n Use -h option for help')
if args[1] == '-C' or args[1] == '-c' or args[1] == '--cricket':
from sports_naarad.cricketAPI import Cricket
if '-f' in args or '--football' in args:
raise ValueError(
'Both Cricket and Football cannot be specifed together!')
if args[2].lower() == 'live-score':
print(Cricket().live_score(type_return='dict'))
elif args[2].lower() == 'fixtures':
tournaments = Cricket().list_matches(type_return='dict')
header = ['Teams', 'Time and Date', 'Venue', 'Result']
for tournament in tournaments:
print("Tournament: {}".format(tournament))
print(
tabulate(tournaments[tournament], headers=header, tablefmt='fancy_grid'))
print('\n')
elif args[2].lower() == 'news':
news = Cricket().news(type_return='dict')
print()
for headline in news:
print('Headline: ' + headline + '\n' +
'link: ' + news[headline] + '\n')
elif args[2].lower() == 'player-stats':
try:
stats = Cricket().get_player_stats(
args[3], type_return='dict')
print('\n')
for stat in stats:
print(stat + ': ' + stats[stat])
except:
raise ValueError('Not a Valid Name!')
else:
raise ValueError(
'Not a Valid Argument! Use -h or --help for help ')
except IndexError:
print("Arguments not according to format. Please see help! Use -h option for help")
def __exit__(self, exc_type=None, exc_value=None, exc_tb=None):
os.reomve(self.path)
def __exit__(self, exc_type=None, exc_value=None, exc_tb=None):
os.reomve(self.path)