def __exit__(self, exc_type, value, traceback):
if exc_type is not None:
return
cache_dir = os.path.dirname(self._cache_fn)
if not os.path.exists(cache_dir):
shutil.makedirs(cache_dir)
tmp_fn = self._cache_fn + '.tmp'
with io.open(tmp_fn, 'w', encoding='utf-8') as outf:
json.dump(self._cache, outf)
os.rename(tmp_fn, self._cache_fn)
def __exit__(self, exc_type, value, traceback):
if exc_type is not None:
return
cache_dir = os.path.dirname(self._cache_fn)
if not os.path.exists(cache_dir):
shutil.makedirs(cache_dir)
tmp_fn = self._cache_fn + '.tmp'
with io.open(tmp_fn, 'w', encoding='utf-8') as outf:
json.dump(self._cache, outf)
os.rename(tmp_fn, self._cache_fn)
def extract_preselect_jpg_fr_RAW(rawimgdir,cp1indx):
import os,sys,subprocess,shutil
#rawimgdir = os.path.abspath(os.path.dirname(rawimgdir))
outdir = os.path.join(rawimgdir,'../../PRESELECT_OUTPUT')
try:
if os.path.isdir(outdir):
shutil.makedirs(outdir)
except:
pass
if cp1indx >= 3:
subprocess.call([
'exiftool',
'-if',
'$jpgfromraw',
'-b',
'-jpgfromraw',
'-w',
'%d/../../PRESELECT_OUTPUT/%f_%ue.jpg',
'-execute',
'-if',
'$previewimage',
'-b',
'-previewimage',
'-w',
'%d/../../PRESELECT_OUTPUT/%f_%ue.jpg',
'-execute',
'-tagsfromfile',
'@',
'-srcfile',
'%d/../../PRESELECT_OUTPUT/%f_%ue.jpg',
'-overwrite_original',
'-common_args',
'-ext',
'CR2',
rawimgdir])
import hashlib
import numpy
shell.prefix("module load bioinfo-tools bbmap samtools perl_modules BioPerl prokka; ")
metasssnake_path = pjoin(os.environ['HOME'], "repos/moritz/metasssnake/")
config['general']['temp_dir'] = os.environ['SNIC_TMP']
if not os.path.exists(config['gtdb']['download']['local']):
call("wget " + config['gtdb']['download']['remote'] + " -O " + config['gtdb']['download']['local'], shell=True)
if not os.path.exists(config['gtdb']['download']['refseq_local']):
call("wget " + config['gtdb']['download']['refseq_remote'] + " -O " + config['gtdb']['download']['refseq_local'], shell=True)
if not os.path.exists(config['gtdb']['download']['genbank_local']):
call("wget " + config['gtdb']['download']['genbank_remote'] + " -O " + config['gtdb']['download']['genbank_local'], shell=True)
if not os.path.exists(config['gtdb']['download']['uba_local']):
shutil.makedirs(config['gtdb']['download']['uba_local'])
call("wget " + config['gtdb']['download']['uba'] + " -O " + config['gtdb']['download']['uba_local'] + "../temp.tar.gz" , shell=True)
call("tar xzvf " + config['gtdb']['download']['uba_local'] + "../temp.tar.gz" , shell=True)
call("mv " + config['gtdb']['download']['uba_local'] + "../UBA*.fsa " + config['gtdb']['download']['uba_local'] , shell=True)
os.remove(config['gtdb']['download']['uba_local'] + "../temp.tar.gz")
def get_taxa(wildcards):
metadata = pandas.read_csv(config['gtdb']['download']['local'], sep = '\t', index_col = 0, low_memory=False)
gtdb_ids = list(metadata.loc[[wildcards.taxon in c for c in metadata.gtdb_taxonomy]].index)
ncbi_fct = lambda g : "{first}/{second}/{third}/{gtdb_id}/pfams.json".format(first = g.split('_')[-1][0:3],second = g.split('_')[-1][3:6], third = g.split('_')[-1][6:9], gtdb_id = g)
uba_fct = lambda g : "UBA/{gtdb_id}/pfams.json".format(gtdb_id = g)
return [ncbi_fct(f) if not "UBA" in f else uba_fct(f) for f in gtdb_ids]
def all_taxa(wildcards):
#print os.environ
#var="exiftool -if '$jpgfromraw' -b -jpgfromraw -w %d%f_%ue.jpg -execute -if '$previewimage' -b -previewimage -w %d%f_%ue.jpg -execute -tagsfromfile @ -srcfile %d%f_%ue.jpg -overwrite_original -common_args --ext jpg DIR"
#exifcmd = list(var.split(' '))
rawimgdir=sys.argv[1]
#rawimgdir = os.path.abspath(os.path.dirname(rawimgdir))
outdir = os.path.join(rawimgdir,'../../OUTPUT')
try:
if os.path.isdir(outdir):
shutil.makedirs(outdir)
except:
pass#print "EXCEPTION DIR"
subprocess.call([
'exiftool',
'-if',
'$jpgfromraw',
'-b',
'-jpgfromraw',
'-w',
'%d/../../OUTPUT/%f_%ue.jpg',
'-execute',
'-if',
def makedirsnocheck(path):
try:
shutil.makedirs(path)
except:
pass
print("[ERROR] Chyba pri poskozovani")
# print(randoms)
return damaged_file_name
if __name__ == '__main__':
if sys.argv[1] == '-h':
print("""argv[1]\t = vstupni obraz ve formatu ppm ve stupnich sedi
*program je urcen k zakladnimu testovani, nekontroluje uzivatelsky vstup"""
)
'''Zpracování obrazu = komprese, poškození, dekomprese, psnr'''
try:
shutil.rmtree('tmp_jpeg2000')
shutil.makedirs('tmp_jpeg2000')
except:
os.makedirs('tmp_jpeg2000/')
ORIGINAL = sys.argv[1]
BITRATE = 1.0
# JPEG 2000
limit_jpeg2000 = 0
img_jp2 = compress_JP2(ORIGINAL, BITRATE)
img_jp2_dx1 = damage_JP2(img_jp2, 0.1)
img_jp2_dx3 = damage_JP2(img_jp2, 0.3)
img_jp2_dx5 = damage_JP2(img_jp2, 0.5)
img_jp2_dx7 = damage_JP2(img_jp2, 0.7)
img_jp2_dx8 = damage_JP2(
