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(